Diff of the two buildlogs: -- --- b1/build.log 2025-07-29 23:37:44.400635683 +0000 +++ b2/build.log 2025-07-30 00:54:45.282005365 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Aug 31 17:42:45 -12 2026 -I: pbuilder-time-stamp: 1788241365 +I: Current time: Wed Jul 30 13:37:48 +14 2025 +I: pbuilder-time-stamp: 1753832268 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -36,52 +36,84 @@ dpkg-source: info: applying better_enums.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/119717/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1326071/tmp/hooks/D01_modify_environment starting +debug: Running on ionos1-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jul 29 23:38 /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/1326071/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1326071/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='d99a6a22902045918757df71681554e2' - 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='119717' - PS1='# ' - PS2='> ' + INVOCATION_ID=c72fac4135e64378b35a187d830215b7 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=1326071 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.kuExrakj/pbuilderrc_fFjz --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.kuExrakj/b1 --logfile b1/build.log rdkit_202503.1-4.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + 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.kuExrakj/pbuilderrc_0opL --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.kuExrakj/b2 --logfile b2/build.log rdkit_202503.1-4.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos15-amd64 6.12.33+deb12-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.33-1~bpo12+1 (2025-07-09) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-37-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.140-1 (2025-05-22) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 12 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/119717/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 12 19:25 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1326071/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -573,7 +605,7 @@ Get: 367 http://deb.debian.org/debian trixie/main amd64 texlive-latex-recommended all 2024.20250309-1 [8745 kB] Get: 368 http://deb.debian.org/debian trixie/main amd64 texlive-pictures all 2024.20250309-1 [17.0 MB] Get: 369 http://deb.debian.org/debian trixie/main amd64 texlive-latex-extra all 2024.20250309-2 [25.2 MB] -Fetched 421 MB in 7s (61.6 MB/s) +Fetched 421 MB in 14s (30.1 MB/s) Preconfiguring packages ... 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 ... 19850 files and directories currently installed.) @@ -1758,8 +1790,8 @@ Setting up tzdata (2025b-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Tue Sep 1 05:44:12 UTC 2026. -Universal Time is now: Tue Sep 1 05:44:12 UTC 2026. +Local time is now: Tue Jul 29 23:42:54 UTC 2025. +Universal Time is now: Tue Jul 29 23:42:54 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libboost-atomic1.83.0:amd64 (1.83.0-4.2) ... @@ -2144,7 +2176,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/rdkit-202503.1/ && 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_202503.1-4_source.changes +I: user script /srv/workspace/pbuilder/1326071/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/1326071/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/rdkit-202503.1/ && 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_202503.1-4_source.changes dpkg-buildpackage: info: source package rdkit dpkg-buildpackage: info: source version 202503.1-4 dpkg-buildpackage: info: source distribution unstable @@ -2268,8 +2304,8 @@ command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. --- Configuring done (1.9s) --- Generating done (1.4s) +-- Configuring done (9.1s) +-- Generating done (4.9s) CMake Warning: Manually-specified variables were not used by the project: @@ -2330,110 +2366,110 @@ command to set the policy and suppress this warning. This warning is for project developers. 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Code/RDStreams/CMakeFiles/RDStreams.dir/streams.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDStreams && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RDSTREAMS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDStreams_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hc.c.o -MF CMakeFiles/hc.dir/hc.c.o.d -o CMakeFiles/hc.dir/hc.c.o -c /build/reproducible-path/rdkit-202503.1/Code/ML/Cluster/Murtagh/hc.c -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/External/GA && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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/build/reproducible-path/rdkit-202503.1/Code/RDGeneral/RDGeneralExceptions.cpp +[ 2%] Building C object Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hcdriver.c.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_HC_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dhc_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-202503.1/Code/ML/Cluster/Murtagh/hcdriver.c -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/External/GA && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dga_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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 External/GA/CMakeFiles/ga.dir/ga/Chromosome.cpp.o -MF CMakeFiles/ga.dir/ga/Chromosome.cpp.o.d -o CMakeFiles/ga.dir/ga/Chromosome.cpp.o -c /build/reproducible-path/rdkit-202503.1/External/GA/ga/Chromosome.cpp -[ 2%] Building CXX object External/GA/CMakeFiles/ga.dir/util/RandomUtil.cpp.o -[ 2%] Building CXX object External/GA/CMakeFiles/ga.dir/util/Util.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/External/GA && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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-Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT External/GA/CMakeFiles/ga.dir/util/Util.cpp.o -MF CMakeFiles/ga.dir/util/Util.cpp.o.d -o CMakeFiles/ga.dir/util/Util.cpp.o -c /build/reproducible-path/rdkit-202503.1/External/GA/util/Util.cpp -[ 2%] Built target inchi_support [ 2%] Linking C shared library ../../../../lib/libRDKithc.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -Wl,--dependency-file=CMakeFiles/hc.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKithc.so.1 -o ../../../../lib/libRDKithc.so.1.2025.03.1 CMakeFiles/hc.dir/hc.c.o CMakeFiles/hc.dir/hcdriver.c.o /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 @@ -2445,9 +2481,9 @@ /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/ga.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitga.so.1 -o ../../lib/libRDKitga.so.1.2025.03.1 CMakeFiles/ga.dir/ga/StringChromosome.cpp.o CMakeFiles/ga.dir/ga/Chromosome.cpp.o CMakeFiles/ga.dir/ga/IntegerStringChromosomePolicy.cpp.o CMakeFiles/ga.dir/ga/BinaryStringChromosomePolicy.cpp.o CMakeFiles/ga.dir/util/RandomUtil.cpp.o 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-I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/RDGeneral/CMakeFiles/testRDValue.dir/testRDValue.cpp.o -MF CMakeFiles/testRDValue.dir/testRDValue.cpp.o.d -o CMakeFiles/testRDValue.dir/testRDValue.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/testRDValue.cpp +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD 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CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/SimDivPickers/DistPicker.cpp -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o -MF CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o.d -o CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DataManip/MetricMatrixCalc/testMatCalc.cpp [ 7%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/MultiFPBReader.cpp.o -MF CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o.d -o CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DataStructs/MultiFPBReader.cpp -[ 7%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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-202503.1/Code/SimDivPickers/MaxMinPicker.cpp +[ 7%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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-202503.1/Code/SimDivPickers/HierarchicalClusterPicker.cpp -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Catalogs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCatalogs_EXPORTS 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Linking CXX executable testMatCalc +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMatCalc.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMatCalc.dir/link.d CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o -o testMatCalc ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 7%] Built target testMatCalc [ 7%] Linking CXX shared library ../../../lib/libRDKitEigenSolvers.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics/EigenSolvers && /usr/bin/cmake -E cmake_link_script CMakeFiles/EigenSolvers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/EigenSolvers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitEigenSolvers.so.1 -o ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics/EigenSolvers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1 ../../../lib/libRDKitEigenSolvers.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 7%] Built target EigenSolvers -[ 7%] Linking CXX executable testMatCalc -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMatCalc.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMatCalc.dir/link.d CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o -o testMatCalc ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 7%] Linking CXX shared library ../../lib/libRDKitCatalogs.so +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Catalogs && /usr/bin/cmake -E cmake_link_script CMakeFiles/Catalogs.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/Catalogs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitCatalogs.so.1 -o ../../lib/libRDKitCatalogs.so.1.2025.03.1 CMakeFiles/Catalogs.dir/Catalog.cpp.o CMakeFiles/Catalogs.dir/CatalogParams.cpp.o CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Catalogs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../lib/libRDKitCatalogs.so.1 ../../lib/libRDKitCatalogs.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 7%] Built target testMatCalc +[ 7%] Built target Catalogs [ 7%] Linking CXX executable testConcurrentQueue cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/testConcurrentQueue.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testConcurrentQueue.dir/link.d CMakeFiles/testConcurrentQueue.dir/testConcurrentQueue.cpp.o -o testConcurrentQueue ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 7%] Built target testConcurrentQueue [ 7%] Linking CXX shared library ../../lib/libRDKitSimDivPickers.so +[ 7%] Linking CXX executable dictTestsCatch +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/dictTestsCatch.dir/link.txt --verbose=1 cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/cmake -E cmake_link_script CMakeFiles/SimDivPickers.dir/link.txt --verbose=1 +[ 7%] Linking CXX executable testMatrices +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMatrices.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/SimDivPickers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSimDivPickers.so.1 -o ../../lib/libRDKitSimDivPickers.so.1.2025.03.1 CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o ../../lib/libRDKithc.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitSimDivPickers.so.1.2025.03.1 ../../lib/libRDKitSimDivPickers.so.1 ../../lib/libRDKitSimDivPickers.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMatrices.dir/link.d CMakeFiles/testMatrices.dir/testMatrices.cpp.o -o testMatrices ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 7%] Built target SimDivPickers make -f Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/SimDivPickers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/SimDivPickers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/DependInfo.cmake "--color=" +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/dictTestsCatch.dir/link.d CMakeFiles/dictTestsCatch.dir/catch_dict.cpp.o -o dictTestsCatch librdkitCatch.a ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/libCatch2.a /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 7%] Built target testMatrices +[ 7%] Built target dictTestsCatch make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' @@ -2629,498 +2681,482 @@ cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o -MF CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o.d -o CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/SimDivPickers/testPickers.cpp [ 7%] Linking CXX executable logTestsCatch cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/logTestsCatch.dir/link.txt --verbose=1 -[ 7%] Linking CXX shared library ../../lib/libRDKitCatalogs.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Catalogs && /usr/bin/cmake -E cmake_link_script CMakeFiles/Catalogs.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/Catalogs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitCatalogs.so.1 -o ../../lib/libRDKitCatalogs.so.1.2025.03.1 CMakeFiles/Catalogs.dir/Catalog.cpp.o CMakeFiles/Catalogs.dir/CatalogParams.cpp.o CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Catalogs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../lib/libRDKitCatalogs.so.1 ../../lib/libRDKitCatalogs.so /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/logTestsCatch.dir/link.d CMakeFiles/logTestsCatch.dir/catch_logs.cpp.o -o logTestsCatch librdkitCatch.a ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/libCatch2.a /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 7%] Built target logTestsCatch -[ 7%] Built target Catalogs -[ 7%] Linking CXX executable testMatrices -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMatrices.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMatrices.dir/link.d 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-Wl,--dependency-file=CMakeFiles/testQuery.dir/link.d CMakeFiles/testQuery.dir/test.cpp.o -o testQuery ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 7%] Built target testQuery [ 8%] Linking CXX shared library ../../lib/libRDKitDataStructs.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/DataStructs.dir/link.txt --verbose=1 -[ 8%] Linking CXX executable dictTestsCatch -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/dictTestsCatch.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/DataStructs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDataStructs.so.1 -o ../../lib/libRDKitDataStructs.so.1.2025.03.1 CMakeFiles/DataStructs.dir/BitVect.cpp.o CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o CMakeFiles/DataStructs.dir/Utils.cpp.o CMakeFiles/DataStructs.dir/base64.cpp.o CMakeFiles/DataStructs.dir/BitOps.cpp.o CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o CMakeFiles/DataStructs.dir/FPBReader.cpp.o CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o CMakeFiles/DataStructs.dir/RealValueVect.cpp.o ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1 ../../lib/libRDKitDataStructs.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 8%] Built target DataStructs make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make Code/Geometry/CMakeFiles/RDGeometryLib.dir/depend -make -f Code/DataStructs/CMakeFiles/testDataStructs.dir/build.make Code/DataStructs/CMakeFiles/testDataStructs.dir/depend -make -f Code/DataStructs/CMakeFiles/testFPB.dir/build.make Code/DataStructs/CMakeFiles/testFPB.dir/depend -make -f Code/DataStructs/CMakeFiles/testMultiFPB.dir/build.make Code/DataStructs/CMakeFiles/testMultiFPB.dir/depend -make -f 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make Code/Geometry/CMakeFiles/RDGeometryLib.dir/build cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/SimDivPickers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/SimDivPickers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make Code/Geometry/CMakeFiles/RDGeometryLib.dir/build -make -f Code/DataStructs/CMakeFiles/testFPB.dir/build.make Code/DataStructs/CMakeFiles/testFPB.dir/build -make -f Code/DataStructs/CMakeFiles/testMultiFPB.dir/build.make Code/DataStructs/CMakeFiles/testMultiFPB.dir/build -make -f Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build.make Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build.make Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build +make -f Code/DataStructs/CMakeFiles/testDataStructs.dir/build.make Code/DataStructs/CMakeFiles/testDataStructs.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f 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object Code/Geometry/CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ML/InfoTheory && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DInfoTheory_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_INFOTHEORY_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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-202503.1/Code/Geometry/Transform3D.cpp -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/Transform2D.cpp.o -MF CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Geometry/Transform2D.cpp +[ 9%] Building CXX object Code/DataStructs/CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB 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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/Geometry/CMakeFiles/RDGeometryLib.dir/point.cpp.o -MF CMakeFiles/RDGeometryLib.dir/point.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/point.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Geometry/point.cpp +make -f Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build.make Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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-202503.1/Code/Geometry/Transform3D.cpp +[ 9%] Building CXX object Code/DataStructs/CMakeFiles/catchDataStructs.dir/catch_tests.cpp.o +[ 9%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/UniformRealValueGrid3D.cpp.o +[ 9%] Building CXX object 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-D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/DataStructs/CMakeFiles/catchDataStructs.dir/catch_tests.cpp.o -MF CMakeFiles/catchDataStructs.dir/catch_tests.cpp.o.d -o CMakeFiles/catchDataStructs.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DataStructs/catch_tests.cpp -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/Transform2D.cpp.o -MF CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Geometry/Transform2D.cpp -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD 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-I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/DiscreteValueVect.cpp.o -MF CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o.d -o CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DataStructs/Wrap/DiscreteValueVect.cpp -[ 11%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o +[ 12%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o +[ 12%] Building CXX object Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/Clustering.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DClustering_EXPORTS -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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-202503.1/Code/ML/Cluster/Murtagh/Clustering.cpp +[ 12%] Building CXX object Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o -MF CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o.d -o CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DataManip/MetricMatrixCalc/Wrap/rdMetricMatrixCalc.cpp cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/SparseIntVect.cpp.o -MF CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o.d -o CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DataStructs/Wrap/SparseIntVect.cpp -[ 11%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/RealValueVect.cpp.o -[ 11%] Building CXX object 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-I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/LeaderPicker.cpp.o -MF CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o.d -o CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/SimDivPickers/Wrap/LeaderPicker.cpp -[ 11%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make Code/GraphMol/CMakeFiles/GraphMol.dir/build -make -f Code/Geometry/CMakeFiles/testGrid.dir/build.make Code/Geometry/CMakeFiles/testGrid.dir/build -make -f Code/Geometry/CMakeFiles/testRealValueGrid.dir/build.make Code/Geometry/CMakeFiles/testRealValueGrid.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/Geometry/CMakeFiles/testTransforms.dir/build.make Code/Geometry/CMakeFiles/testTransforms.dir/build -make -f Code/Geometry/CMakeFiles/geometryTestsCatch.dir/build.make Code/Geometry/CMakeFiles/geometryTestsCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/Geometry/CMakeFiles/geometryTestsCatch.dir/build.make Code/Geometry/CMakeFiles/geometryTestsCatch.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/Features/CMakeFiles/testBaseFeatures.dir/build.make Code/Features/CMakeFiles/testBaseFeatures.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build.make Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/Geometry/CMakeFiles/testGrid.dir/build.make Code/Geometry/CMakeFiles/testGrid.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 13%] Building CXX object Code/Features/CMakeFiles/testBaseFeatures.dir/testFeatures.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Features && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time 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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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Geometry/CMakeFiles/testTransforms.dir/testTransforms.cpp.o -MF CMakeFiles/testTransforms.dir/testTransforms.cpp.o.d -o CMakeFiles/testTransforms.dir/testTransforms.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Geometry/testTransforms.cpp +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Geometry/CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o -MF CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o.d -o 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+cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Geometry/CMakeFiles/testGrid.dir/testGrid.cpp.o -MF CMakeFiles/testGrid.dir/testGrid.cpp.o.d -o CMakeFiles/testGrid.dir/testGrid.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Geometry/testGrid.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/Features/CMakeFiles/testBaseFeatures.dir/build.make Code/Features/CMakeFiles/testBaseFeatures.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build.make Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build +make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make Code/GraphMol/CMakeFiles/GraphMol.dir/build +[ 14%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/UniformRealValueGrid3D.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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-202503.1/Code/Geometry/Wrap/UniformGrid3D.cpp +make -f Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/UniformRealValueGrid3D.cpp.o -MF CMakeFiles/rdGeometry.dir/UniformRealValueGrid3D.cpp.o.d -o CMakeFiles/rdGeometry.dir/UniformRealValueGrid3D.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Geometry/Wrap/UniformRealValueGrid3D.cpp +[ 14%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build +[ 14%] Building CXX object Code/Numerics/CMakeFiles/testConrec.dir/testConrec.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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-202503.1/Code/Geometry/Wrap/rdGeometry.cpp +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Numerics/CMakeFiles/testConrec.dir/testConrec.cpp.o -MF CMakeFiles/testConrec.dir/testConrec.cpp.o.d -o CMakeFiles/testConrec.dir/testConrec.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Numerics/testConrec.cpp +[ 14%] Building CXX object Code/Geometry/CMakeFiles/testRealValueGrid.dir/testRealValueGrid.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Geometry/CMakeFiles/testRealValueGrid.dir/testRealValueGrid.cpp.o -MF CMakeFiles/testRealValueGrid.dir/testRealValueGrid.cpp.o.d -o CMakeFiles/testRealValueGrid.dir/testRealValueGrid.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Geometry/testRealValueGrid.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 12%] Building CXX object Code/Numerics/Alignment/CMakeFiles/Alignment.dir/AlignPoints.cpp.o -[ 12%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryAtom.cpp.o -[ 12%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryBond.cpp.o -[ 12%] Building CXX object 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/QueryOps.cpp.o -MF CMakeFiles/GraphMol.dir/QueryOps.cpp.o.d -o CMakeFiles/GraphMol.dir/QueryOps.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/QueryOps.cpp +[ 16%] Linking CXX shared library ../../lib/libRDKitChemicalFeatures.so +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/ChemicalFeatures.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/Data/CMakeFiles/cQuantize.dir/cQuantize.cpp.o -MF CMakeFiles/cQuantize.dir/cQuantize.cpp.o.d -o CMakeFiles/cQuantize.dir/cQuantize.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ML/Data/cQuantize.cpp -[ 16%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/MolPickler.cpp.o -MF CMakeFiles/GraphMol.dir/MolPickler.cpp.o.d -o CMakeFiles/GraphMol.dir/MolPickler.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolPickler.cpp +[ 16%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK 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Code/GraphMol/CMakeFiles/GraphMol.dir/MonomerInfo.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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/usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 20%] Built target geometryTestsCatch [ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Atropisomers.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 20%] Built target testRealValueGrid [ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolProps.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/MolProps.cpp.o -MF CMakeFiles/GraphMol.dir/MolProps.cpp.o.d -o CMakeFiles/GraphMol.dir/MolProps.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolProps.cpp -[ 20%] Linking CXX shared module ../../../rdkit/ML/Data/cQuantize.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ML/Data && /usr/bin/cmake -E cmake_link_script CMakeFiles/cQuantize.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/cQuantize.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/ML/Data/cQuantize.so CMakeFiles/cQuantize.dir/cQuantize.cpp.o ../../../lib/libRDKitInfoTheory.so.1.2025.03.1 ../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 -ldl /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 +[ 20%] Linking CXX executable testAlignment +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAlignment.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Trajectory/Trajectory.cpp +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/lex.yysmiles.cpp.o -MF CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o.d -o CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse/lex.yysmiles.cpp -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/sln.tab.cpp.o -MF CMakeFiles/SLNParse.dir/sln.tab.cpp.o.d -o CMakeFiles/SLNParse.dir/sln.tab.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SLNParse/sln.tab.cpp +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB 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-ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/AtropisomerBond.cpp.o -MF CMakeFiles/CIPLabeler.dir/configs/AtropisomerBond.cpp.o.d -o CMakeFiles/CIPLabeler.dir/configs/AtropisomerBond.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/configs/AtropisomerBond.cpp +[ 23%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/Queries.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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-ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/Rule1a.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/rules/Rule1a.cpp [ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/Rule1b.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/rules/Rule1b.cpp [ 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-D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/rules/Rule2.cpp +[ 23%] Building CXX object Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT 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/build/reproducible-path/rdkit-202503.1/Code/ChemicalFeatures/Wrap/FreeChemicalFeature.cpp [ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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-202503.1/Code/GraphMol/CIPLabeler/rules/Rule3.cpp [ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o @@ -3329,63 +3365,63 @@ cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/SequenceRule.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/rules/SequenceRule.cpp -[ 24%] Linking CXX executable tableTestsCatch -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/tableTestsCatch.dir/link.txt --verbose=1 [ 24%] Linking CXX shared library ../../../lib/libRDKitMolCatalog.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolCatalog.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection 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../../../lib/libRDKitMolCatalog.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 24%] Linking CXX shared library ../../../lib/libRDKitPartialCharges.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_link_script CMakeFiles/PartialCharges.dir/link.txt --verbose=1 -[ 24%] Built target tableTestsCatch +[ 24%] Built target MolCatalog +make -f Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build.make Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolCatalog/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu 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CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o.d -o CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolCatalog/Wrap/rdMolCatalog.cpp +[ 24%] Linking CXX executable tableTestsCatch +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/tableTestsCatch.dir/link.txt --verbose=1 [ 24%] Linking CXX shared library ../../../lib/libRDKitTrajectory.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_link_script CMakeFiles/Trajectory.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/PartialCharges.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitPartialCharges.so.1 -o ../../../lib/libRDKitPartialCharges.so.1.2025.03.1 CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 24%] Linking CXX shared library ../../../lib/libRDKitPartialCharges.so +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_link_script CMakeFiles/PartialCharges.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/Trajectory.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitTrajectory.so.1 -o ../../../lib/libRDKitTrajectory.so.1.2025.03.1 CMakeFiles/Trajectory.dir/Trajectory.cpp.o ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitPartialCharges.so.1.2025.03.1 ../../../lib/libRDKitPartialCharges.so.1 ../../../lib/libRDKitPartialCharges.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/libRDKitTrajectory.so.1 ../../../lib/libRDKitTrajectory.so -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolCatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolCatalog.so.1 -o ../../../lib/libRDKitMolCatalog.so.1.2025.03.1 CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolCatalog.so.1.2025.03.1 ../../../lib/libRDKitMolCatalog.so.1 ../../../lib/libRDKitMolCatalog.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 24%] Built target Trajectory -[ 24%] Built target MolCatalog make -f Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/depend -[ 24%] Built target PartialCharges -make -f Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build.make Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/depend make -f Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/Numerics/Optimizer /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics/Optimizer /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolCatalog/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu 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"--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build.make Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build.make Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build +make -f Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 24%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/LinearSearch.cpp.o -[ 24%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o -[ 24%] Building CXX object Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o [ 24%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/Numerics/Optimizer/CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o -MF CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o.d -o CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Numerics/Optimizer/BFGSOpt.cpp -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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-ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/rdTrajectory.cpp.o -MF CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o.d -o CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/rdTrajectory.cpp +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tableTestsCatch.dir/link.d CMakeFiles/tableTestsCatch.dir/catch_periodictable.cpp.o -o tableTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitGraphMol.so.1.2025.03.1 /usr/lib/libCatch2.a ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/PartialCharges.dir/link.d -Wl,-z,relro -Wl,-z,now -shared 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-I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/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-202503.1/Code/GraphMol/PartialCharges/Wrap/rdPartialCharges.cpp [ 24%] Linking CXX shared library ../../../lib/libRDKitSubgraphs.so @@ -3394,6 +3430,30 @@ cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs && 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-I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o -MF CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o.d -o CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ShapeHelpers/ShapeUtils.cpp [ 24%] Linking CXX shared library ../../../lib/libRDKitOptimizer.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/cmake -E cmake_link_script CMakeFiles/Optimizer.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -MF CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o.d -o CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Numerics/Optimizer/testOptimizer.cpp [ 24%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/AngleConstraint.cpp.o [ 24%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/ForceField.cpp.o -[ 24%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/DistanceConstraints.cpp.o -[ 24%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/AngleConstraints.cpp.o -[ 24%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/DistanceConstraint.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall 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-ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -MF CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o.d -o CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Numerics/Optimizer/testOptimizer.cpp cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/ForceField.cpp.o -MF CMakeFiles/ForceField.dir/ForceField.cpp.o.d -o CMakeFiles/ForceField.dir/ForceField.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/ForceField.cpp +[ 24%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/AngleConstraints.cpp.o +[ 24%] Building CXX object 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/DistanceConstraint.cpp.o -MF CMakeFiles/ForceField.dir/DistanceConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/DistanceConstraint.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/DistanceConstraint.cpp +[ 24%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/DistanceConstraints.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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-I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/Utils.cpp.o -MF CMakeFiles/ForceField.dir/UFF/Utils.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/Utils.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/UFF/Utils.cpp -[ 25%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB 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-ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/TorsionConstraint.cpp.o -MF CMakeFiles/ForceField.dir/TorsionConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/TorsionConstraint.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/TorsionConstraint.cpp cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time 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Code/ForceField/CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/Substruct/CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o -MF CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o.d -o CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Substruct/SubstructMatch.cpp +[ 26%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o.d -o CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Substruct/SubstructUtils.cpp +[ 26%] Linking CXX shared library ../../../lib/libRDKitCIPLabeler.so +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/cmake -E cmake_link_script CMakeFiles/CIPLabeler.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/CIPLabeler.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitCIPLabeler.so.1 -o ../../../lib/libRDKitCIPLabeler.so.1.2025.03.1 CMakeFiles/CIPLabeler.dir/CIPMol.cpp.o 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Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdCIPLabeler_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 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/usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1 ../../../lib/libRDKitMolTransforms.so -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/GenericGroups.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitGenericGroups.so.1 -o ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o 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-DShapeHelpers_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o -MF CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o.d -o CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ShapeHelpers/ShapeUtils.cpp -[ 27%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -[ 27%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o -cd 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-I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/Substruct/CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o -MF CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o.d -o CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Substruct/SubstructMatch.cpp -[ 28%] Linking CXX executable testOptimizer -[ 28%] Linking CXX shared module ../../../../rdkit/Chem/rdPartialCharges.so +[ 26%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ 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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-202503.1/Code/ForceField/MMFF/Nonbonded.cpp +[ 27%] Linking CXX shared module ../../../../rdkit/Chem/rdPartialCharges.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdPartialCharges.dir/link.txt --verbose=1 -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/cmake -E cmake_link_script CMakeFiles/testOptimizer.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall 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/usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSLNParse.so.1.2025.03.1 ../../../lib/libRDKitSLNParse.so.1 ../../../lib/libRDKitSLNParse.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 28%] Built target SLNParse +[ 27%] Built target SLNParse make -f Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build.make Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SLNParse/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/DependInfo.cmake "--color=" +[ 28%] Linking CXX shared module ../../../rdkit/Chem/rdChemicalFeatures.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build.make Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdChemicalFeatures.dir/link.txt --verbose=1 make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 28%] Building CXX object Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o cd 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-Werror=format-security -fcf-protection -Wdate-time -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/Wrap/CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o -MF CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o.d -o CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SLNParse/Wrap/rdSLNParse.cpp -[ 29%] Linking CXX shared module ../../../rdkit/Chem/rdtrajectory.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdtrajectory.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdChemicalFeatures.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdChemicalFeatures.so CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o ../../../lib/libRDKitChemicalFeatures.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 29%] Built target rdtrajectory -[ 29%] Linking CXX shared library ../../../lib/libRDKitShapeHelpers.so +[ 28%] Built target rdChemicalFeatures +[ 28%] Linking CXX shared library ../../../lib/libRDKitShapeHelpers.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/ShapeHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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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Linking CXX shared module ../../../../rdkit/Chem/rdCIPLabeler.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdCIPLabeler.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 29%] Built target ShapeHelpers +[ 28%] Built target ShapeHelpers make -f Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ShapeHelpers/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu 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../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 29%] Built target rdCIPLabeler -[ 29%] Linking CXX shared module ../../../rdkit/Chem/rdqueries.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdqueries.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 29%] Built target rdqueries -[ 29%] Linking CXX shared library ../../lib/libRDKitForceField.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/cmake -E cmake_link_script CMakeFiles/ForceField.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/ForceField.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitForceField.so.1 -o ../../lib/libRDKitForceField.so.1.2025.03.1 CMakeFiles/ForceField.dir/ForceField.cpp.o CMakeFiles/ForceField.dir/AngleConstraint.cpp.o CMakeFiles/ForceField.dir/AngleConstraints.cpp.o CMakeFiles/ForceField.dir/DistanceConstraint.cpp.o CMakeFiles/ForceField.dir/DistanceConstraints.cpp.o CMakeFiles/ForceField.dir/PositionConstraint.cpp.o CMakeFiles/ForceField.dir/TorsionConstraint.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/Inversions.cpp.o CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o CMakeFiles/ForceField.dir/UFF/Params.cpp.o CMakeFiles/ForceField.dir/UFF/Utils.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/Params.cpp.o ../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitForceField.so.1.2025.03.1 ../../lib/libRDKitForceField.so.1 ../../lib/libRDKitForceField.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 29%] Built target ForceField -[ 29%] Linking CXX shared library ../../../lib/libRDKitMolInterchange.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolInterchange.dir/link.txt --verbose=1 -[ 30%] Linking CXX shared module ../../../../rdkit/Chem/rdMolCatalog.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolCatalog.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMolCatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolCatalog.so CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o ../../../../lib/libRDKitMolCatalog.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../../lib/libRDKitCatalogs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolInterchange.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolInterchange.so.1 -o ../../../lib/libRDKitMolInterchange.so.1.2025.03.1 CMakeFiles/MolInterchange.dir/Parser.cpp.o CMakeFiles/MolInterchange.dir/Writer.cpp.o ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -[ 30%] Built target rdMolCatalog -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolInterchange.so.1.2025.03.1 ../../../lib/libRDKitMolInterchange.so.1 ../../../lib/libRDKitMolInterchange.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 30%] Built target MolInterchange -make -f Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build.make Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInterchange/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build.make Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 30%] Building CXX object Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolInterchange_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/External/rapidjson-1.1.0/include -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o -MF CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o.d -o CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInterchange/Wrap/rdMolInterchange.cpp -[ 30%] Linking CXX shared module ../../../../rdkit/Chem/rdSLNParse.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSLNParse.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdSLNParse.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdSLNParse.so CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o ../../../../lib/libRDKitSLNParse.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 30%] Built target rdSLNParse -[ 31%] Linking CXX shared library ../../../lib/libRDKitSmilesParse.so +[ 29%] Linking CXX shared library ../../../lib/libRDKitSmilesParse.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/SmilesParse.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/SmilesParse.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSmilesParse.so.1 -o ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 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/CanonicalizeStereoGroups.cpp.o CMakeFiles/SmilesParse.dir/SmilesJSONParsers.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.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1 ../../../lib/libRDKitSmilesParse.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 31%] Built target SmilesParse +[ 29%] Built target SmilesParse make -f Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolcpTest.dir/depend make -f Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolIterTest.dir/depend -make -f Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/depend -make -f Code/GraphMol/CMakeFiles/queryTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/queryTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolcpTest.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/depend +make -f Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/depend +make -f Code/GraphMol/CMakeFiles/queryTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/queryTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/depend cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolIterTest.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/SmilesParse/CMakeFiles/v2smiTestCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/v2smiTestCatch.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/DependInfo.cmake "--color=" +make -f 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/v2smiTestCatch.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/depend -make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/depend -make -f Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/depend -make -f Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/depend make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/cptest.cpp +[ 29%] Building CXX object Code/GraphMol/CMakeFiles/graphmolIterTest.dir/itertest.cpp.o +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/GraphMol/SmilesParse/CMakeFiles/v2smiTestCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/v2smiTestCatch.dir/depend +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolIterTest.dir/itertest.cpp.o -MF CMakeFiles/graphmolIterTest.dir/itertest.cpp.o.d -o CMakeFiles/graphmolIterTest.dir/itertest.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/itertest.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build -make -f Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 29%] Building CXX object Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/v2smiTestCatch.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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 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-DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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/queryTestsCatch.dir/catch_queries.cpp.o -MF CMakeFiles/queryTestsCatch.dir/catch_queries.cpp.o.d -o CMakeFiles/queryTestsCatch.dir/catch_queries.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/catch_queries.cpp +make -f Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/depend +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/test2.cpp.o -MF CMakeFiles/smiTest2.dir/test2.cpp.o.d -o 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-Wl,--dependency-file=CMakeFiles/rdBase.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/rdBase.so CMakeFiles/rdBase.dir/RDBase.cpp.o ../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 -ldl /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 32%] Built target rdBase +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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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Built target MolInterchange +make -f Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build.make Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInterchange/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/DependInfo.cmake "--color=" [ 32%] Linking CXX shared module ../../../../rdkit/Chem/rdMolTransforms.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap && 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Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolInterchange_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/External/rapidjson-1.1.0/include -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include 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../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 32%] Built target testPartialCharges +[ 32%] Linking CXX executable smiTest2 +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiTest2.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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/usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 32%] Built target subgraphsCatch +[ 32%] Linking CXX executable graphmolcpTest +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolcpTest.dir/link.txt --verbose=1 +[ 33%] Linking CXX executable v2smiTestCatch +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/v2smiTestCatch.dir/link.txt --verbose=1 +[ 33%] Linking CXX executable graphmolIterTest +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolIterTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 33%] Built target v2smiTestCatch +[ 33%] Linking CXX executable molbundleTestsCatch +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/molbundleTestsCatch.dir/link.txt --verbose=1 +[ 33%] Linking CXX executable testSubgraphs2 +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSubgraphs2.dir/link.txt --verbose=1 +[ 33%] Linking CXX executable graphmolMemTest1 +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolMemTest1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molbundleTestsCatch.dir/link.d CMakeFiles/molbundleTestsCatch.dir/catch_molbundle.cpp.o -o molbundleTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 /usr/lib/libCatch2.a ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 33%] Built target molbundleTestsCatch +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testSubgraphs2.dir/link.d CMakeFiles/testSubgraphs2.dir/test2.cpp.o -o testSubgraphs2 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmolMemTest1.dir/link.d CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o -o graphmolMemTest1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 33%] Built target testSubgraphs2 +[ 33%] Built target graphmolMemTest1 +[ 33%] Linking CXX shared library ../../../lib/libRDKitSubstructMatch.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/SubstructMatch.dir/link.txt --verbose=1 -[ 32%] Linking CXX shared module ../../../rdkit/rdBase.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDBoost/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdBase.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/SubstructMatch.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSubstructMatch.so.1 -o ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1 ../../../lib/libRDKitSubstructMatch.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 32%] Built target SubstructMatch +[ 33%] Built target SubstructMatch make -f Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build.make 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"--color=" -make -f Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/depend -make -f Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/depend +make -f Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/DependInfo.cmake "--color=" -make -f 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build -make -f Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build +make -f Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +cd 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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-202503.1/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleM6.cpp +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 34%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o 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Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o -MF CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o.d -o CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolChemicalFeatures/FeatureParser.cpp +[ 39%] Linking CXX shared module ../../../../rdkit/Chem/rdMolInterchange.so +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/Wrap && /usr/bin/cmake -E cmake_link_script 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Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Abbreviations/AbbreviationsUtils.cpp [ 39%] Linking CXX shared library ../../../lib/libRDKitReducedGraphs.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/ReducedGraphs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/ReducedGraphs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitReducedGraphs.so.1 -o ../../../lib/libRDKitReducedGraphs.so.1.2025.03.1 CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl @@ -3950,22 +3981,47 @@ cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ReducedGraphs/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/DependInfo.cmake "--color=" make[4]: Leaving directory 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-Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o -MF CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o.d -o CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ReducedGraphs/Wrap/rdReducedGraphs.cpp [ 39%] Building CXX object Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/test1.cpp.o -MF CMakeFiles/testReducedGraphs.dir/test1.cpp.o.d -o CMakeFiles/testReducedGraphs.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ReducedGraphs/test1.cpp +[ 39%] Linking CXX executable moliteratorTestsCatch +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/moliteratorTestsCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 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/usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 39%] Built target moliteratorTestsCatch [ 39%] Linking CXX shared library ../../../lib/libRDKitFragCatalog.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/FragCatalog.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/FragCatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFragCatalog.so.1 -o ../../../lib/libRDKitFragCatalog.so.1.2025.03.1 CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFragCatalog.so.1.2025.03.1 ../../../lib/libRDKitFragCatalog.so.1 ../../../lib/libRDKitFragCatalog.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 39%] Built target FragCatalog +[ 39%] Linking CXX shared library ../../../lib/libRDKitMolChemicalFeatures.so +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolChemicalFeatures.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolChemicalFeatures.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolChemicalFeatures.so.1 -o ../../../lib/libRDKitMolChemicalFeatures.so.1.2025.03.1 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../../../lib/libRDKitMolChemicalFeatures.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 39%] Built target MolChemicalFeatures +make -f Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolChemicalFeatures/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 39%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o +[ 39%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB 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CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o.d -o CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolChemicalFeatures/Wrap/rdMolChemicalFeatures.cpp +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/MolChemicalFeature.cpp.o -MF CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o.d -o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeature.cpp +[ 39%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o +[ 39%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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-202503.1/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeatureFactory.cpp +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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-202503.1/Code/GraphMol/MolChemicalFeatures/Wrap/ChemicalFeatureUtils.cpp [ 39%] Linking CXX shared library ../../../lib/libRDKitAbbreviations.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/cmake -E cmake_link_script CMakeFiles/Abbreviations.dir/link.txt --verbose=1 -[ 39%] Built target FragCatalog /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/Abbreviations.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitAbbreviations.so.1 -o ../../../lib/libRDKitAbbreviations.so.1.2025.03.1 CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitAbbreviations.so.1.2025.03.1 ../../../lib/libRDKitAbbreviations.so.1 ../../../lib/libRDKitAbbreviations.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' @@ -3982,78 +4038,63 @@ cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/ForceFieldHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/ForceFieldHelpers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitForceFieldHelpers.so.1 -o ../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleContribs.cpp.o ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../lib/libRDKitForceFieldHelpers.so.1 ../../../lib/libRDKitForceFieldHelpers.so -[ 39%] Linking CXX shared library ../../../lib/libRDKitMolChemicalFeatures.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolChemicalFeatures.dir/link.txt --verbose=1 -[ 39%] Linking CXX shared library ../../../lib/libRDKitMolAlign.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolAlign.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 39%] Built target ForceFieldHelpers make -f Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/build.make Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/depend make -f Code/DistGeom/CMakeFiles/DistGeometry.dir/build.make Code/DistGeom/CMakeFiles/DistGeometry.dir/depend -make -f Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build.make Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/ForceField /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/depend +make -f Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build.make Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/DistGeom /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DistGeom /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DistGeom/CMakeFiles/DistGeometry.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/MolInteractionFields/CMakeFiles/MolInteractionFields.dir/build.make 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Code/GraphMol/MolInteractionFields/CMakeFiles/MolInteractionFields.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInteractionFields /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInteractionFields /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInteractionFields/CMakeFiles/MolInteractionFields.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/build.make Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/build +make -f Code/DistGeom/CMakeFiles/DistGeometry.dir/build.make Code/DistGeom/CMakeFiles/DistGeometry.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolChemicalFeatures.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolChemicalFeatures.so.1 -o ../../../lib/libRDKitMolChemicalFeatures.so.1.2025.03.1 CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolChemicalFeatures.so.1.2025.03.1 ../../../lib/libRDKitMolChemicalFeatures.so.1 ../../../lib/libRDKitMolChemicalFeatures.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolInteractionFields/CMakeFiles/MolInteractionFields.dir/build.make Code/GraphMol/MolInteractionFields/CMakeFiles/MolInteractionFields.dir/build +make -f Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/build.make Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build.make Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/DistGeom/CMakeFiles/DistGeometry.dir/build.make Code/DistGeom/CMakeFiles/DistGeometry.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build.make 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/Wrap/CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o -MF CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o.d -o CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp +make -f Code/GraphMol/MolInteractionFields/CMakeFiles/MolInteractionFields.dir/build.make 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/build/reproducible-path/rdkit-202503.1/External/CoordGen/Wrap/rdCoordGen.cpp -[ 40%] Linking CXX shared library ../../../lib/libRDKitFingerprints.so +[ 40%] Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/FilterCatalog.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/FilterCatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFilterCatalog.so.1 -o ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 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.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1 ../../../lib/libRDKitFilterCatalog.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 40%] 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-202503.1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap 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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 -Drdfiltercatalog_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/rdfiltercatalog.cpp.o -MF CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o.d -o CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/Wrap/rdfiltercatalog.cpp +[ 41%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfiltercatalog_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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-202503.1/Code/GraphMol/FilterCatalog/Wrap/FilterCatalog.cpp +[ 41%] Linking CXX shared library ../../../lib/libRDKitFingerprints.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/Fingerprints.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/Fingerprints.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFingerprints.so.1 -o ../../../lib/libRDKitFingerprints.so.1.2025.03.1 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.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1 ../../../lib/libRDKitFingerprints.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 40%] Built target Fingerprints +[ 41%] Built target Fingerprints make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/depend make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' @@ -4095,61 +4152,28 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f 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-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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o -MF 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-DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMHFPFingerprint_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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-202503.1/Code/GraphMol/Fingerprints/Wrap/MHFPWrapper.cpp -[ 40%] Linking CXX executable testReducedGraphs -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReducedGraphs.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testReducedGraphs.dir/link.d CMakeFiles/testReducedGraphs.dir/test1.cpp.o -o testReducedGraphs ../../../lib/libRDKitReducedGraphs.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 40%] Built target testReducedGraphs -[ 40%] Linking CXX shared module ../../../../rdkit/Chem/rdReducedGraphs.so +[ 41%] Linking CXX shared module ../../../../rdkit/Chem/rdReducedGraphs.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdReducedGraphs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdReducedGraphs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdReducedGraphs.so CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o ../../../../lib/libRDKitReducedGraphs.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 40%] Built target rdReducedGraphs -[ 40%] Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/FilterCatalog.dir/link.txt --verbose=1 -[ 40%] Linking CXX executable graphmolqueryTest -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolqueryTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmolqueryTest.dir/link.d CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o -o graphmolqueryTest ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 40%] Built target graphmolqueryTest -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/FilterCatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFilterCatalog.so.1 -o ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 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.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1 ../../../lib/libRDKitFilterCatalog.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 40%] 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-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build.make Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 41%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o -[ 41%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfiltercatalog_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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-202503.1/Code/GraphMol/FilterCatalog/Wrap/FilterCatalog.cpp -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfiltercatalog_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/rdfiltercatalog.cpp.o -MF CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o.d -o CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/Wrap/rdfiltercatalog.cpp +[ 41%] Built target rdReducedGraphs [ 41%] Linking CXX executable ForceFieldsCatch cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/cmake -E cmake_link_script CMakeFiles/ForceFieldsCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/ForceFieldsCatch.dir/link.d CMakeFiles/ForceFieldsCatch.dir/catch_tests.cpp.o -o ForceFieldsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../lib/libRDKitForceField.so.1.2025.03.1 ../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 41%] Built target ForceFieldsCatch -[ 41%] Linking CXX executable testSLNParse -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSLNParse.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testSLNParse.dir/link.d CMakeFiles/testSLNParse.dir/test.cpp.o -o testSLNParse ../../../lib/libRDKitSLNParse.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 41%] Built target testSLNParse -[ 41%] Linking CXX shared module ../../../../rdkit/Chem/rdMolChemicalFeatures.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolChemicalFeatures.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMolChemicalFeatures.dir/link.d -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.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 41%] Linking CXX executable graphmolqueryTest +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolqueryTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmolqueryTest.dir/link.d CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o -o graphmolqueryTest ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 41%] Built target rdMolChemicalFeatures +[ 41%] Built target graphmolqueryTest [ 41%] Linking CXX shared library ../../lib/libRDKitDistGeometry.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeometry.dir/link.txt --verbose=1 -[ 41%] Linking CXX executable smaTest1 -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smaTest1.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/DistGeometry.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDistGeometry.so.1 -o ../../lib/libRDKitDistGeometry.so.1.2025.03.1 CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o CMakeFiles/DistGeometry.dir/DistViolationContribs.cpp.o CMakeFiles/DistGeometry.dir/ChiralViolationContribs.cpp.o ../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../lib/libRDKitForceField.so.1.2025.03.1 ../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitDistGeometry.so.1.2025.03.1 ../../lib/libRDKitDistGeometry.so.1 ../../lib/libRDKitDistGeometry.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' @@ -4161,32 +4185,49 @@ cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/DistGeom/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DistGeom/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build.make Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build -make -f Code/DistGeom/CMakeFiles/testDistGeom.dir/build.make Code/DistGeom/CMakeFiles/testDistGeom.dir/build +make -f 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/Wrap/CMakeFiles/DistGeom.dir/DistGeom.cpp.o -MF CMakeFiles/DistGeom.dir/DistGeom.cpp.o.d -o CMakeFiles/DistGeom.dir/DistGeom.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DistGeom/Wrap/DistGeom.cpp [ 41%] Building CXX object Code/DistGeom/CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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-202503.1/Code/GraphMol/DistGeomHelpers/EmbedderUtils.cpp +[ 41%] Building CXX object Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DistGeom.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DistGeom/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDistGeom_EXPORTS -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/Wrap/CMakeFiles/DistGeom.dir/DistGeom.cpp.o -MF CMakeFiles/DistGeom.dir/DistGeom.cpp.o.d -o CMakeFiles/DistGeom.dir/DistGeom.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DistGeom/Wrap/DistGeom.cpp +[ 41%] Linking CXX shared module ../../../../rdkit/Chem/rdMolChemicalFeatures.so +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolChemicalFeatures.dir/link.txt --verbose=1 +[ 41%] Linking CXX executable testDistGeom +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDistGeom.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 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../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 41%] Built target smaTest1 +[ 41%] Built target testDistGeom +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMolChemicalFeatures.dir/link.d -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.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 41%] Built target rdMolChemicalFeatures +[ 41%] Linking CXX executable testSLNParse +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSLNParse.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testSLNParse.dir/link.d CMakeFiles/testSLNParse.dir/test.cpp.o -o testSLNParse ../../../lib/libRDKitSLNParse.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 41%] Built target testSLNParse +[ 41%] Linking CXX executable smaTest1 +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smaTest1.dir/link.txt --verbose=1 [ 41%] Linking CXX shared library ../../../lib/libRDKitMolInteractionFields.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInteractionFields && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolInteractionFields.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/smaTest1.dir/link.d CMakeFiles/smaTest1.dir/smatest.cpp.o -o smaTest1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 41%] Built target smaTest1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolInteractionFields.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolInteractionFields.so.1 -o ../../../lib/libRDKitMolInteractionFields.so.1.2025.03.1 CMakeFiles/MolInteractionFields.dir/MIFDescriptors.cpp.o ../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInteractionFields && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolInteractionFields.so.1.2025.03.1 ../../../lib/libRDKitMolInteractionFields.so.1 ../../../lib/libRDKitMolInteractionFields.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' @@ -4199,26 +4240,6 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 41%] Building CXX object Code/GraphMol/MolInteractionFields/Wrap/CMakeFiles/rdMIF.dir/rdMIF.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInteractionFields/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMIF_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/MolInteractionFields/Wrap/CMakeFiles/rdMIF.dir/rdMIF.cpp.o -MF CMakeFiles/rdMIF.dir/rdMIF.cpp.o.d -o CMakeFiles/rdMIF.dir/rdMIF.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInteractionFields/Wrap/rdMIF.cpp -[ 41%] Linking CXX shared module ../../../../rdkit/Chem/rdForceFieldHelpers.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdForceFieldHelpers.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdForceFieldHelpers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdForceFieldHelpers.so CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o ../../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 41%] Built target rdForceFieldHelpers -[ 41%] Linking CXX shared module ../../../../rdkit/Chem/rdAbbreviations.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdAbbreviations.dir/link.txt --verbose=1 -[ 41%] Linking CXX executable testDistGeom -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDistGeom.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testDistGeom.dir/link.d CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -o testDistGeom ../../lib/libRDKitDistGeometry.so.1.2025.03.1 ../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../lib/libRDKitForceField.so.1.2025.03.1 ../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdAbbreviations.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdAbbreviations.so CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o ../../../../lib/libRDKitAbbreviations.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 41%] Built target testDistGeom -[ 41%] Built target rdAbbreviations -[ 41%] Linking CXX shared module ../../../rdkit/Chem/rdCoordGen.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/External/CoordGen/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdCoordGen.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdCoordGen.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdCoordGen.so CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 -ldl /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 41%] Built target rdCoordGen [ 41%] Linking CXX shared library ../../../lib/libRDKitDepictor.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_link_script CMakeFiles/Depictor.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/Depictor.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDepictor.so.1 -o ../../../lib/libRDKitDepictor.so.1.2025.03.1 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/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl @@ -4227,77 +4248,97 @@ [ 41%] Built target Depictor make -f External/INCHI-API/CMakeFiles/RDInchiLib.dir/build.make External/INCHI-API/CMakeFiles/RDInchiLib.dir/depend make -f Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/depend -make -f Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/build.make Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd 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../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 42%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/normalize.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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CMakeFiles/MolHash.dir/normalize.cpp.o.d -o CMakeFiles/MolHash.dir/normalize.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolHash/normalize.cpp +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdCoordGen.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdCoordGen.so CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 -ldl /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 42%] Built target DistGeom +[ 42%] Built target rdCoordGen [ 42%] Linking CXX shared module ../../../rdkit/ForceField/rdForceField.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField/Wrap && /usr/bin/cmake -E 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/usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 42%] Built target rdAbbreviations [ 42%] Linking CXX shared library ../../../lib/libRDKitDistGeomHelpers.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeomHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/DistGeomHelpers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDistGeomHelpers.so.1 -o ../../../lib/libRDKitDistGeomHelpers.so.1.2025.03.1 CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitDistGeometry.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDistGeomHelpers.so.1.2025.03.1 ../../../lib/libRDKitDistGeomHelpers.so.1 ../../../lib/libRDKitDistGeomHelpers.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 42%] Built target DistGeomHelpers -[ 42%] Linking CXX shared library ../../../lib/libRDKitMolHash.so +[ 43%] Linking CXX shared module ../../../../rdkit/Chem/rdMHFPFingerprint.so +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMHFPFingerprint.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMHFPFingerprint.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMHFPFingerprint.so CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o ../../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 43%] Built target rdMHFPFingerprint +[ 43%] Linking CXX shared library ../../../lib/libRDKitMolHash.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolHash.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolHash.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolHash.so.1 -o ../../../lib/libRDKitMolHash.so.1.2025.03.1 CMakeFiles/MolHash.dir/hashfunctions.cpp.o CMakeFiles/MolHash.dir/normalize.cpp.o ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolHash.so.1.2025.03.1 ../../../lib/libRDKitMolHash.so.1 ../../../lib/libRDKitMolHash.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 42%] Built target MolHash +[ 43%] Built target MolHash make -f Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build.make Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolHash/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-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-202503.1/obj-x86_64-linux-gnu' -[ 42%] Building CXX object Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o +[ 43%] Building CXX object Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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-202503.1/Code/GraphMol/MolHash/Wrap/rdMolHash.cpp -[ 43%] Linking CXX shared module ../../../../rdkit/Chem/rdMHFPFingerprint.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMHFPFingerprint.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMHFPFingerprint.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMHFPFingerprint.so CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o ../../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 43%] Linking CXX shared module ../../../../rdkit/Chem/rdFingerprintGenerator.so +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdFingerprintGenerator.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdFingerprintGenerator.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdFingerprintGenerator.so CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o ../../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 43%] Built target rdMHFPFingerprint +[ 43%] Built target rdFingerprintGenerator [ 43%] Linking CXX shared library ../../lib/libRDKitRDInchiLib.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/External/INCHI-API && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDInchiLib.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/RDInchiLib.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDInchiLib.so.1 -o ../../lib/libRDKitRDInchiLib.so.1.2025.03.1 CMakeFiles/RDInchiLib.dir/inchi.cpp.o /usr/lib/x86_64-linux-gnu/libinchi.so ../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../lib/libRDKitAlignment.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl @@ -4317,11 +4358,6 @@ /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdDepictor.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdDepictor.so CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o ../../../../lib/libRDKitDepictor.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 43%] Built target rdDepictor -[ 43%] Linking CXX shared module ../../../../rdkit/Chem/rdFingerprintGenerator.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdFingerprintGenerator.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdFingerprintGenerator.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdFingerprintGenerator.so CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o ../../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 43%] Built target rdFingerprintGenerator [ 43%] Linking CXX shared module ../../../../rdkit/Chem/rdMIF.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInteractionFields/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMIF.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMIF.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMIF.so CMakeFiles/rdMIF.dir/rdMIF.cpp.o ../../../../lib/libRDKitMolInteractionFields.so.1.2025.03.1 ../../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../../lib/libRDKitPartialCharges.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 -ldl /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 @@ -4346,62 +4382,62 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 43%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o [ 43%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o -[ 43%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/CDXMLParser.cpp.o -MF CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o.d -o CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/CDXMLParser.cpp [ 43%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileParser.cpp.o -[ 43%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o -[ 43%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDWriter.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/Mol2FileParser.cpp.o -MF CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o.d -o CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/Mol2FileParser.cpp [ 43%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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-202503.1/Code/GraphMol/FileParsers/SDWriter.cpp [ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileParser.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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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/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/CMLWriter.cpp.o -MF CMakeFiles/FileParsers.dir/CMLWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/CMLWriter.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/CMLWriter.cpp +[ 45%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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 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-I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/XYZFileParser.cpp.o -MF CMakeFiles/FileParsers.dir/XYZFileParser.cpp.o.d -o CMakeFiles/FileParsers.dir/XYZFileParser.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/XYZFileParser.cpp +[ 45%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB 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-ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/MaeWriter.cpp.o -MF CMakeFiles/FileParsers.dir/MaeWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/MaeWriter.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/MaeWriter.cpp +[ 45%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o +[ 45%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB 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CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/ProximityBonds.cpp cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/SequenceParsers.cpp.o -MF CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o.d -o CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/SequenceParsers.cpp +[ 45%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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-202503.1/Code/GraphMol/FileParsers/SequenceWriters.cpp +[ 45%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SVGParser.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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-202503.1/Code/GraphMol/FileParsers/SVGParser.cpp +[ 46%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PNGParser.cpp.o +[ 46%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o +[ 46%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o +[ 46%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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-202503.1/Code/GraphMol/FileParsers/PNGParser.cpp cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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-202503.1/Code/GraphMol/FileParsers/MultithreadedMolSupplier.cpp cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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-202503.1/Code/GraphMol/FileParsers/MultithreadedSmilesMolSupplier.cpp @@ -4424,411 +4460,443 @@ [ 47%] Built target FileParsers make -f External/CoordGen/CMakeFiles/testCoordGen.dir/build.make External/CoordGen/CMakeFiles/testCoordGen.dir/depend make -f Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build.make Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/depend -make -f Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build.make Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/depend -make -f Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/depend -make -f Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/External/CoordGen /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/External/CoordGen /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/External/CoordGen/CMakeFiles/testCoordGen.dir/DependInfo.cmake "--color=" +make -f Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build.make Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/depend +make -f Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/depend cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/ForceField/UFF /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField/UFF /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/CMakeFiles/hanoiTest.dir/build.make Code/GraphMol/CMakeFiles/hanoiTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField/MMFF /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/depend +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build.make Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/depend +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/CMakeFiles/molBundleTest.dir/build.make Code/GraphMol/CMakeFiles/molBundleTest.dir/depend +make -f External/CoordGen/CMakeFiles/testCoordGen.dir/build.make External/CoordGen/CMakeFiles/testCoordGen.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build.make Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/molBundleTest.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/CMakeFiles/graphmolOrganometallicsCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolOrganometallicsCatch.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol 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-E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolOrganometallicsCatch.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/depend +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build.make Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/CMakeFiles/canonTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/canonTestsCatch.dir/depend +make -f Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/CMakeFiles/pickleTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/pickleTestsCatch.dir/depend -make -f Code/GraphMol/CMakeFiles/molopsTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/molopsTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/depend +make -f Code/GraphMol/CMakeFiles/hanoiTest.dir/build.make Code/GraphMol/CMakeFiles/hanoiTest.dir/depend +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 48%] Building CXX object External/CoordGen/CMakeFiles/testCoordGen.dir/test.cpp.o make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/pickleTestsCatch.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build +[ 48%] Building CXX object Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/External/CoordGen && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DIN_COORDGEN -DIN_MAEPARSER -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT External/CoordGen/CMakeFiles/testCoordGen.dir/test.cpp.o -MF CMakeFiles/testCoordGen.dir/test.cpp.o.d -o CMakeFiles/testCoordGen.dir/test.cpp.o -c /build/reproducible-path/rdkit-202503.1/External/CoordGen/test.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/canonTestsCatch.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/depend -make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/depend -make -f Code/GraphMol/SmilesParse/CMakeFiles/nontetrahedralCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/nontetrahedralCatch.dir/depend +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 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-ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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-202503.1/Code/ForceField/MMFF/testMMFFForceField.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/molopsTestsCatch.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build +[ 48%] Building CXX object Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -MF CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o.d -o CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/molopstest.cpp +[ 48%] Building CXX object Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField/UFF && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o -MF CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o.d -o CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/UFF/testUFFForceField.cpp +make -f Code/GraphMol/CMakeFiles/molBundleTest.dir/build.make Code/GraphMol/CMakeFiles/molBundleTest.dir/depend +[ 48%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -MF CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o.d -o CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/testChirality.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/GraphMol/CMakeFiles/testSGroup.dir/build.make Code/GraphMol/CMakeFiles/testSGroup.dir/depend +[ 48%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o +[ 48%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o -MF CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o.d -o CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/testPickler.cpp +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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-202503.1/Code/GraphMol/testPicklerGlobalSettings.cpp +make -f Code/GraphMol/CMakeFiles/hanoiTest.dir/build.make Code/GraphMol/CMakeFiles/hanoiTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/molBundleTest.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/depend -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/nontetrahedralCatch.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/Depictor/CMakeFiles/depictorCatch.dir/build.make Code/GraphMol/Depictor/CMakeFiles/depictorCatch.dir/depend -make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/depend -make -f Code/GraphMol/FileParsers/CMakeFiles/testAtropisomers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testAtropisomers.dir/depend -make -f Code/GraphMol/FileParsers/CMakeFiles/testSquiggleDoubleBonds.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testSquiggleDoubleBonds.dir/depend +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/testSGroup.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/depend -make -f Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/depend +make -f Code/GraphMol/CMakeFiles/test-valgrind.dir/build.make Code/GraphMol/CMakeFiles/test-valgrind.dir/depend +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build.make Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/test-valgrind.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testAtropisomers.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/depend +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 48%] Building CXX object Code/GraphMol/CMakeFiles/hanoiTest.dir/hanoitest.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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-ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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-202503.1/Code/GraphMol/resMolSupplierTest.cpp +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o -MF CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o.d -o CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/testMolBundle.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/GraphMol/CMakeFiles/test-valgrind.dir/build.make Code/GraphMol/CMakeFiles/test-valgrind.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build.make 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/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/GraphMol/CMakeFiles/graphmolOrganometallicsCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolOrganometallicsCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 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-isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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-202503.1/Code/GraphMol/testSGroup.cpp +make -f Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/depend +[ 48%] Building CXX object Code/GraphMol/CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f External/CoordGen/CMakeFiles/testCoordGen.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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o -MF CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o.d -o CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/test-valgrind.cpp +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o -MF CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o.d -o 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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/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-202503.1/Code/GraphMol/catch_organometallics.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/build +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 48%] Building CXX object Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o -MF CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o.d -o CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/catch_sgroups.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-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-202503.1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/depend +make -f Code/GraphMol/CMakeFiles/pickleTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/pickleTestsCatch.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/GraphMol/CMakeFiles/molopsTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/molopsTestsCatch.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/build +[ 49%] Building CXX object Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/catch_chirality.cpp.o +[ 49%] Building CXX object Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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-202503.1/Code/GraphMol/catch_adjustquery.cpp +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/depend +make -f Code/GraphMol/SmilesParse/CMakeFiles/nontetrahedralCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/nontetrahedralCatch.dir/depend make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +cd 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-I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/canonTestsCatch.dir/catch_canon.cpp.o -MF CMakeFiles/canonTestsCatch.dir/catch_canon.cpp.o.d -o CMakeFiles/canonTestsCatch.dir/catch_canon.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/catch_canon.cpp +[ 49%] Building CXX object Code/GraphMol/CMakeFiles/molopsTestsCatch.dir/catch_molops.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB 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/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 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"--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +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-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/canonTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/canonTestsCatch.dir/build -make -f Code/GraphMol/CMakeFiles/molopsTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/molopsTestsCatch.dir/build +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o -MF CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o.d -o CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/testMolSupplier.cpp +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/ReactionRunner.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/ReactionRunner.cpp +[ 51%] Built target test-valgrind +[ 51%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o +cd 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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-202503.1/Code/GraphMol/ChemReactions/Enumerate/EvenSamplePairs.cpp +[ 51%] Linking CXX executable testGeneralFileReader +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 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+make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 52%] Built target graphmoltestPicklerGlobalSetting 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-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' 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51%] Linking CXX executable testMol2ToMol -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMol2ToMol.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMol2ToMol.dir/link.d CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -o testMol2ToMol ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 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-Wl,--dependency-file=CMakeFiles/testUFFForceField.dir/link.d CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o -o testUFFForceField ../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 52%] Built target testUFFForceField make -f Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu 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Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o +[ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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-202503.1/Code/GraphMol/FileParsers/molfile_stereo_catch.cpp -[ 52%] Built target testTplParser +[ 53%] Linking CXX executable canonTestsCatch +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/canonTestsCatch.dir/link.txt 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/usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 53%] Built target canonTestsCatch make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC 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/usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 52%] Built target testSquiggleDoubleBonds -[ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_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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/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/DependInfo.cmake "--color=" +[ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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/connectTheDotsTest.dir/connectTheDots_catch.cpp.o -MF CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o.d -o CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/connectTheDots_catch.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/v2_suppliers_catch.cpp.o 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-D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/v2_suppliers_catch.cpp.o -MF CMakeFiles/v2MolSuppliers.dir/v2_suppliers_catch.cpp.o.d -o CMakeFiles/v2MolSuppliers.dir/v2_suppliers_catch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/v2_suppliers_catch.cpp -[ 52%] Linking CXX executable testMultithreadedMolSupplier -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMultithreadedMolSupplier.dir/link.txt --verbose=1 -[ 53%] Linking CXX executable graphmolOrganometallicsCatch -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolOrganometallicsCatch.dir/link.txt --verbose=1 -[ 53%] Linking CXX executable molopsTestsCatch -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/molopsTestsCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMultithreadedMolSupplier.dir/link.d CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o -o testMultithreadedMolSupplier ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitRDStreams.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 -ldl /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 +[ 53%] Linking CXX executable resMolSupplierTest +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/resMolSupplierTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/resMolSupplierTest.dir/link.d CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o -o resMolSupplierTest ../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitEigenSolvers.so.1.2025.03.1 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/v2FileParsersCatchTest.dir/DependInfo.cmake "--color=" @@ -4837,11 +4905,6 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/v2FileParsersCatchTest.dir/v2_file_parsers_catch.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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/v2FileParsersCatchTest.dir/v2_file_parsers_catch.cpp.o -MF CMakeFiles/v2FileParsersCatchTest.dir/v2_file_parsers_catch.cpp.o.d -o CMakeFiles/v2FileParsersCatchTest.dir/v2_file_parsers_catch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/v2_file_parsers_catch.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmolOrganometallicsCatch.dir/link.d CMakeFiles/graphmolOrganometallicsCatch.dir/catch_organometallics.cpp.o -o graphmolOrganometallicsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../lib/libRDKitAlignment.so.1.2025.03.1 ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 53%] Built target graphmolOrganometallicsCatch -[ 53%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/ReactionRunner.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/ReactionRunner.cpp [ 53%] Linking CXX executable molBundleTest cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/molBundleTest.dir/link.txt --verbose=1 make -f Code/GraphMol/FileParsers/CMakeFiles/atropisomersCatch.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/atropisomersCatch.dir/depend @@ -4850,67 +4913,37 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/atropisomersCatch.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/atropisomersCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat 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../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 53%] Built target molopsTestsCatch [ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/atropisomersCatch.dir/atropisomers_catch.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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/atropisomersCatch.dir/atropisomers_catch.cpp.o -MF CMakeFiles/atropisomersCatch.dir/atropisomers_catch.cpp.o.d -o CMakeFiles/atropisomersCatch.dir/atropisomers_catch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/atropisomers_catch.cpp -[ 53%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/PreprocessRxn.cpp.o -MF CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o.d -o CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/PreprocessRxn.cpp -[ 53%] Linking CXX executable testAtropisomers -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAtropisomers.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/x86_64-linux-gnu/libmaeparser.so -make -f Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/depend make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 53%] Linking CXX executable testCoordGen +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testCoordGen.dir/link.d CMakeFiles/testCoordGen.dir/test.cpp.o -o testCoordGen 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 53%] Built target molBundleTest +make -f Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f 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/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/DependInfo.cmake "--color=" +[ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/multithreaded_supplier_catch.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/multithreaded_supplier_catch.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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/multithreadedSupplierCatchTest.dir/multithreaded_supplier_catch.cpp.o -MF CMakeFiles/multithreadedSupplierCatchTest.dir/multithreaded_supplier_catch.cpp.o.d -o CMakeFiles/multithreadedSupplierCatchTest.dir/multithreaded_supplier_catch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/multithreaded_supplier_catch.cpp [ 53%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/test1.cpp.o cd 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 53%] Built target testGeneralFileReader +[ 53%] Built target nontetrahedralCatch make -f Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/DependInfo.cmake "--color=" @@ -4919,39 +4952,27 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 53%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 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-o CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Enumerate/EvenSamplePairs.cpp -[ 53%] Linking CXX executable testUFFForceField -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField/UFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testUFFForceField.dir/link.txt --verbose=1 -[ 53%] Linking CXX executable hanoiTest -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/hanoiTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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-202503.1/obj-x86_64-linux-gnu' -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/hanoiTest.dir/link.d CMakeFiles/hanoiTest.dir/hanoitest.cpp.o -o hanoiTest ../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../lib/libRDKitAlignment.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 53%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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-202503.1/Code/GraphMol/ChemTransforms/catch_tests.cpp -[ 53%] Built target hanoiTest make -f 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../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/hanoiTest.dir/link.d CMakeFiles/hanoiTest.dir/hanoitest.cpp.o -o hanoiTest ../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 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-DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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-202503.1/Code/GraphMol/FragCatalog/test1.cpp cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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-I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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-202503.1/Code/GraphMol/FragCatalog/Wrap/FragCatalog.cpp -[ 54%] Linking CXX executable connectTheDotsTest -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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-202503.1/Code/GraphMol/Descriptors/Lipinski.cpp +[ 54%] Built target testSGroup 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-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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-202503.1/Code/GraphMol/Fingerprints/test1.cpp +[ 54%] Linking CXX executable XYZFileParserCatchTest +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/XYZFileParserCatchTest.dir/link.txt --verbose=1 +[ 54%] Linking CXX executable testDepictor +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDepictor.dir/link.txt --verbose=1 make -f 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/usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 57%] Linking CXX executable testMMFFForceField -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceField.dir/link.txt --verbose=1 -[ 57%] Built target filterCatalogTest -[ 57%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MORSE.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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/usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 55%] Built target testTplParser make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/MMFF /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF 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CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFHelpers.cpp -[ 59%] Linking CXX executable testMHFPFingerprint -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMHFPFingerprint.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/v2FileParsersCatchTest.dir/link.d CMakeFiles/v2FileParsersCatchTest.dir/v2_file_parsers_catch.cpp.o -o v2FileParsersCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2025.03.1 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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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o -MF CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o.d -o CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/MMFF/testMultiThread.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMHFPFingerprint.dir/link.d CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o -o testMHFPFingerprint ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so +[ 56%] Linking CXX executable atropisomersCatch +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/atropisomersCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/atropisomersCatch.dir/link.d CMakeFiles/atropisomersCatch.dir/atropisomers_catch.cpp.o -o atropisomersCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 59%] Linking CXX shared module ../../../../rdkit/Chem/rdfragcatalog.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdfragcatalog.dir/link.txt --verbose=1 -[ 59%] Built target testMHFPFingerprint +[ 56%] Built target atropisomersCatch make -f Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/UFF /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 59%] Building CXX object Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o +[ 56%] Building CXX object Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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-202503.1/Code/GraphMol/ForceFieldHelpers/UFF/testUFFHelpers.cpp -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdfragcatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdfragcatalog.so CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o ../../../../lib/libRDKitFragCatalog.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 56%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB 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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-202503.1/Code/GraphMol/FragCatalog/Wrap/FragCatalog.cpp +[ 56%] Linking CXX executable testMHFPFingerprint +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMHFPFingerprint.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMHFPFingerprint.dir/link.d CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o -o testMHFPFingerprint ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 56%] Built target testMHFPFingerprint make -f Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/build.make Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/depend -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-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/CrystalFF /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/DependInfo.cmake "--color=" -[ 59%] Built target rdfragcatalog -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-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/build.make Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/build -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 56%] Building CXX object Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o -MF CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o.d -o CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalFF.cpp +[ 56%] Linking CXX executable molfileStereoCatchTest +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molfileStereoCatchTest.dir/link.d CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o -o molfileStereoCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitCIPLabeler.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 56%] Built target molfileStereoCatchTest +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-202503.1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/build.make Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/depend +[ 56%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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-202503.1/Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp +[ 56%] Linking CXX executable testMolWriter +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolWriter.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMolWriter.dir/link.d CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -o testMolWriter ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 56%] Built target testMolWriter +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-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/DistGeomHelpers/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/DependInfo.cmake "--color=" -[ 59%] Building CXX object Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o -MF CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o.d -o CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalFF.cpp make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/build -[ 59%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 56%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/Wrap/CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o -MF CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o.d -o CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/DistGeomHelpers/Wrap/rdDistGeom.cpp make -f Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' @@ -5274,89 +5220,125 @@ make[4]: Leaving directory 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-I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o -MF CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o.d -o CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolAlign/testMolAlign.cpp +[ 56%] Linking CXX executable testMMFFForceField +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceField.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o -MF CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o.d -o CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolAlign/catch_tests.cpp +[ 56%] Linking CXX executable v2MolSuppliers +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/v2MolSuppliers.dir/link.txt --verbose=1 +[ 56%] Linking CXX executable cdxmlParserCatchTest +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/cdxmlParserCatchTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/v2MolSuppliers.dir/link.d CMakeFiles/v2MolSuppliers.dir/v2_suppliers_catch.cpp.o -o v2MolSuppliers ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 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make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 59%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/testFeatures.cpp.o +[ 56%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/testFeatures.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 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cmake_link_script CMakeFiles/graphmoltestPickler.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmoltestPickler.dir/link.d CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o -o graphmoltestPickler ../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../lib/libRDKitMolTransforms.so.1.2025.03.1 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Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o -MF CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o.d -o CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/RepeatUnit.cpp -[ 63%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/PartitionSet.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RASCALMCES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRascalMCES_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External 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chemTransformsTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so +[ 59%] Linking CXX executable testCrystalForceField +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCrystalForceField.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testCrystalForceField.dir/link.d CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o -o testCrystalForceField ../../../../lib/libRDKitDistGeomHelpers.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../../lib/libRDKitDistGeometry.so.1.2025.03.1 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-DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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-202503.1/Code/GraphMol/Trajectory/trajectoryTest.cpp -[ 64%] Linking CXX executable testMMFFForceFieldHelpersMultiThread -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/link.txt --verbose=1 -[ 64%] Linking CXX executable testCrystalForceField -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCrystalForceField.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/link.d 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/usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 64%] Built target testMMFFForceFieldHelpersMultiThread +[ 59%] Built target testPropertyLists 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-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange 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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/GraphMol/FMCS/CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o -MF CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o.d -o CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/MaximumCommonSubgraph.cpp -[ 64%] Linking CXX executable testChemTransforms -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/testChemTransforms.dir/link.txt --verbose=1 -[ 64%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFMCS_EXPORTS 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/usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 64%] Built target testChemTransforms +[ 60%] Built target fpGenTestCatch 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-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange 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&& /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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testFeatures.dir/link.d CMakeFiles/testFeatures.dir/testFeatures.cpp.o -o testFeatures ../../../lib/libRDKitMolChemicalFeatures.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolAlign.dir/link.txt --verbose=1 +[ 64%] Built target testMMFFForceFieldHelpers +[ 64%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalCluster.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RASCALMCES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRascalMCES_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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 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-I/build/reproducible-path/rdkit-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/MolDraw2DDetails.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/MolDraw2DDetails.cpp -[ 69%] Linking CXX executable molHashCatchTest -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolHash && 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-Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolEnumerator.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolEnumerator.so.1 -o ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 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-I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/DrawAnnotation.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawAnnotation.cpp -[ 69%] Linking CXX executable molInterchangeTest1 -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/molInterchangeTest1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molInterchangeTest1.dir/link.d CMakeFiles/molInterchangeTest1.dir/test1.cpp.o -o molInterchangeTest1 ../../../lib/libRDKitMolInterchange.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 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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-202503.1/Code/GraphMol/MolDraw2D/DrawMol.cpp -[ 70%] Linking CXX executable distGeomHelpersCatch -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/distGeomHelpersCatch.dir/link.txt --verbose=1 -[ 70%] Linking CXX executable testFingerprints -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFingerprints.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.cpp -[ 71%] Linking CXX shared library ../../../lib/libRDKitRascalMCES.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/cmake -E cmake_link_script CMakeFiles/RascalMCES.dir/link.txt --verbose=1 -[ 72%] Linking CXX shared library ../../../lib/libRDKitFMCS.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_link_script CMakeFiles/FMCS.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection 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../../../lib/libRDKitFMCS.so.1 ../../../lib/libRDKitFMCS.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 72%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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-202503.1/Code/GraphMol/Deprotect/deprotectTest.cpp -[ 72%] Built target FMCS +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 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../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 -ldl /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testEnumeration.dir/link.d CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o -o testEnumeration ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 72%] Built target testMIF -[ 72%] Building CXX object Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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-202503.1/Code/GraphMol/Deprotect/Wrap/DeprotectWrap.cpp -[ 72%] Built target testEnumeration -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMMPA.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMMPA.so CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o ../../../../lib/libRDKitMMPA.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 64%] Linking CXX executable chemTransformsTestCatch +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/chemTransformsTestCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/chemTransformsTestCatch.dir/link.d CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o -o chemTransformsTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 72%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/DrawTextNotFT.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawTextNotFT.cpp -[ 72%] Built target rdMMPA -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testDistGeomHelpers.dir/link.d CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o -o testDistGeomHelpers ../../../lib/libRDKitDistGeomHelpers.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitDistGeometry.so.1.2025.03.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so +[ 64%] Linking CXX shared library ../../../lib/libRDKitMMPA.so +[ 64%] Built target chemTransformsTestCatch +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_link_script CMakeFiles/MMPA.dir/link.txt --verbose=1 +[ 64%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/MolDraw2DSVG.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/MolDraw2DSVG.cpp +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MMPA.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMMPA.so.1 -o ../../../lib/libRDKitMMPA.so.1.2025.03.1 CMakeFiles/MMPA.dir/MMPA.cpp.o ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMMPA.so.1.2025.03.1 ../../../lib/libRDKitMMPA.so.1 ../../../lib/libRDKitMMPA.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 72%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/TautomerCatalog/TautomerCatalogEntry.cpp.o -MF CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o.d -o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogEntry.cpp -[ 72%] Built target testDistGeomHelpers -[ 72%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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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/DrawTextSVG.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawTextSVG.cpp -[ 73%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/TautomerCatalog/TautomerCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogParams.cpp -make -f Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/depend +[ 64%] Built target MMPA +make -f Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build +make -f Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 73%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -cd 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/PositionVariation.cpp +[ 64%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/Seed.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/FMCS/CMakeFiles/FMCS.dir/Seed.cpp.o -MF CMakeFiles/FMCS.dir/Seed.cpp.o.d -o CMakeFiles/FMCS.dir/Seed.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/Seed.cpp +[ 64%] Linking CXX shared library ../../../lib/libRDKitMolProcessing.so +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolProcessing.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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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../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 -ldl /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolProcessing.so.1.2025.03.1 ../../../lib/libRDKitMolProcessing.so.1 ../../../lib/libRDKitMolProcessing.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 64%] Built target MolProcessing +make -f Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build.make Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build +make -f Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build.make Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 74%] Building CXX object Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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-I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/FMCS/CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o -MF CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o.d -o CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/MaximumCommonSubgraph.cpp +[ 64%] Linking CXX executable molHashCatchTest +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_link_script CMakeFiles/molHashCatchTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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-202503.1/Code/GraphMol/Deprotect/Wrap/DeprotectWrap.cpp +[ 65%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o +cd 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-fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o -MF CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o.d -o CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/SubstructMatchCustom.cpp +[ 65%] Linking CXX executable testMMPA +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMPA.dir/link.txt --verbose=1 +[ 65%] Linking CXX executable molInterchangeTest1 +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/molInterchangeTest1.dir/link.txt --verbose=1 +[ 65%] Linking CXX executable testUFFForceFieldHelpers +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testUFFForceFieldHelpers.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMMPA.dir/link.d CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o -o testMMPA ../../../lib/libRDKitMMPA.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 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Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 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/usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build.make Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 76%] Building CXX object Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/testFMCS.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_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-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES/CMakeFiles/testRascalMCES.dir/DependInfo.cmake "--color=" +[ 65%] Built target testReactionFingerprints +[ 65%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK 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cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/DependInfo.cmake "--color=" +[ 66%] Built target rdfragcatalog +[ 66%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/lap_a_la_scipy.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RASCALMCES_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/RascalMCES/CMakeFiles/RascalMCES.dir/PartitionSet.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RASCALMCES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRascalMCES_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time 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Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 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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/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-202503.1/Code/GraphMol/Descriptors/OxidationNumbers.cpp +[ 68%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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 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-I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/RDF.cpp.o -MF CMakeFiles/Descriptors.dir/RDF.cpp.o.d -o CMakeFiles/Descriptors.dir/RDF.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/RDF.cpp +[ 69%] Linking CXX executable graphmolTestsCatch +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolTestsCatch.dir/link.txt --verbose=1 +[ 69%] Building CXX object 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-I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/AcidBaseCatalogEntry.cpp.o -MF CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o.d -o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.cpp +[ 73%] Linking CXX shared module ../../../../rdkit/Chem/rdDeprotect.so +cd 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../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 73%] Built target rdDeprotect +[ 73%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/DrawTextFT.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawTextFT.cpp +[ 73%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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-202503.1/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.cpp +[ 73%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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-202503.1/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.cpp +[ 73%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/TransformCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.cpp +[ 73%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/DrawTextFTSVG.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawTextFTSVG.cpp +[ 73%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong 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CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawTextFTCairo.cpp +[ 73%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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-202503.1/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.cpp In file included from /usr/include/c++/14/vector:62, from /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp:15: 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]', @@ -6053,594 +5930,551 @@ /usr/include/c++/14/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))); | ^ -make -f Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu 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-I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/testWHIM.cpp.o -MF CMakeFiles/testWHIM.dir/testWHIM.cpp.o.d -o CMakeFiles/testWHIM.dir/testWHIM.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/testWHIM.cpp -[ 79%] Linking CXX executable fileParsersTest1 -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileParsersTest1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 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-DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/TautomerCatalog/TautomerCatalogEntry.cpp.o -MF CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o.d -o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o -c 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/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFMCS.so.1.2025.03.1 ../../../lib/libRDKitFMCS.so.1 ../../../lib/libRDKitFMCS.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 79%] Built target fileParsersTest1 -make -f Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/depend +[ 74%] 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-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu 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/usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitRascalMCES.so.1.2025.03.1 ../../../lib/libRDKitRascalMCES.so.1 ../../../lib/libRDKitRascalMCES.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/build.make Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/build +[ 76%] Built target RascalMCES +make -f Code/GraphMol/RascalMCES/CMakeFiles/testRascalMCES.dir/build.make Code/GraphMol/RascalMCES/CMakeFiles/testRascalMCES.dir/depend +make -f Code/GraphMol/RascalMCES/CMakeFiles/testRascalCluster.dir/build.make Code/GraphMol/RascalMCES/CMakeFiles/testRascalCluster.dir/depend make[4]: Entering directory 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"--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 80%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 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-I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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-202503.1/Code/GraphMol/RascalMCES/mces_catch.cpp +[ 76%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/testRascalCluster.dir/mces_cluster_catch.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB 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CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 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/usr/lib/x86_64-linux-gnu/libmaeparser.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1 ../../../lib/libRDKitMolStandardize.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 80%] Built target MolStandardize +[ 77%] Built target MolStandardize make -f Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/depend make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/depend make -f Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/depend -make -f Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build.make 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/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/depend +make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/depend -make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/depend -make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizePipelineTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizePipelineTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build.make Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/depend +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd 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/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizePipelineTest.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/depend make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build -make -f Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/build -make -f 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/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_TAUTOMERQUERY_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DTautomerQuery_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/TautomerQuery/CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o -MF CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o.d -o CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/TautomerQuery/TautomerQuery.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build +[ 77%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/test1.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_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/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 83%] Built target rdDeprotect -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 83%] Built target MarvinParser +make -f Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build.make Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build +[ 78%] Building CXX object Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o +cd 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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/molStandardizePipelineTest.dir/testPipeline.cpp.o -MF CMakeFiles/molStandardizePipelineTest.dir/testPipeline.cpp.o.d -o CMakeFiles/molStandardizePipelineTest.dir/testPipeline.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/testPipeline.cpp +[ 80%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Charge.cpp.o +[ 80%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd 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-DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/Validate.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Validate.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Validate.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Wrap/Validate.cpp make 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-I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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-202503.1/Code/GraphMol/MolStandardize/Wrap/Charge.cpp +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libcairo.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolDraw2D.so.1.2025.03.1 ../../../lib/libRDKitMolDraw2D.so.1 ../../../lib/libRDKitMolDraw2D.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 86%] Built target MolDraw2D -[ 86%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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-202503.1/Code/GraphMol/Wrap/ForwardSDMolSupplier.cpp -[ 86%] Linking CXX executable testRascalMCES -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRascalMCES.dir/link.txt --verbose=1 -[ 86%] Linking CXX executable molChargeTest -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molChargeTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testRascalMCES.dir/link.d CMakeFiles/testRascalMCES.dir/mces_catch.cpp.o -o testRascalMCES ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitRascalMCES.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 82%] Built target MolDraw2D +make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/depend +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/rxnTestCatch.dir/link.d CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o -o rxnTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitChemReactions.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 86%] Built target testRascalMCES -[ 86%] Linking CXX shared module ../../../../rdkit/Chem/rdFMCS.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdFMCS.dir/link.txt --verbose=1 -[ 86%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Edge.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Edge.cpp.o -MF CMakeFiles/testCIPLabeler.dir/Edge.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/Edge.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/Edge.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molChargeTest.dir/link.d CMakeFiles/molChargeTest.dir/testCharge.cpp.o -o molChargeTest ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/DependInfo.cmake "--color=" +[ 82%] Built target rxnTestCatch +make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 86%] Built target molChargeTest -[ 86%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Bond.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/Bond.cpp.o -MF CMakeFiles/rdchem.dir/Bond.cpp.o.d -o CMakeFiles/rdchem.dir/Bond.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/Bond.cpp -[ 86%] Linking CXX shared library ../../../lib/libRDKitO3AAlign.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/O3AAlign.dir/link.txt --verbose=1 -[ 86%] Linking CXX executable molFragmentTest -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molFragmentTest.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/O3AAlign.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitO3AAlign.so.1 -o ../../../lib/libRDKitO3AAlign.so.1.2025.03.1 CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o ../../../lib/libRDKitDescriptors.so.1.2025.03.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../lib/libRDKitPartialCharges.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitO3AAlign.so.1.2025.03.1 ../../../lib/libRDKitO3AAlign.so.1 ../../../lib/libRDKitO3AAlign.so -[ 86%] Linking CXX executable molValidateTest -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molValidateTest.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdFMCS.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdFMCS.so CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o ../../../../lib/libRDKitFMCS.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 86%] Built target rdFMCS +make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 82%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/test1.cpp.o 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Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeWriter.cpp.o -MF CMakeFiles/rdmolfiles.dir/MaeWriter.cpp.o.d -o CMakeFiles/rdmolfiles.dir/MaeWriter.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/MaeWriter.cpp -[ 88%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS 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Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Pipeline.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/Pipeline.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Pipeline.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Pipeline.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Wrap/Pipeline.cpp +[ 83%] Linking CXX shared library ../../../lib/libRDKitScaffoldNetwork.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_link_script CMakeFiles/ScaffoldNetwork.dir/link.txt --verbose=1 -cd 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-ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/RingInfo.cpp.o -MF CMakeFiles/rdchem.dir/RingInfo.cpp.o.d -o CMakeFiles/rdchem.dir/RingInfo.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/RingInfo.cpp -[ 89%] Linking CXX shared library ../../../lib/libRDKitTautomerQuery.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_link_script CMakeFiles/TautomerQuery.dir/link.txt --verbose=1 +[ 83%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Edge.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ 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Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Edge.cpp.o -MF CMakeFiles/testCIPLabeler.dir/Edge.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/Edge.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/Edge.cpp +[ 83%] Linking CXX shared module ../../../../rdkit/Chem/rdMolEnumerator.so +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolEnumerator.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMolEnumerator.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o 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../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 83%] Built target rdMolEnumerator /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 83%] Built target ScaffoldNetwork +make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f 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Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/catch_tests.cpp -make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/depend +[ 86%] Built target TautomerQuery +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-202503.1/obj-x86_64-linux-gnu' -cd 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-I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/TautomerQuery/catch_tests.cpp +[ 86%] Linking CXX executable testMrvToMol +[ 86%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/cmake -E cmake_link_script 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molTautomerTest +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molTautomerTest.dir/link.txt --verbose=1 In file included from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, @@ -6669,6 +6503,29 @@ /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:39: note: '' declared here 55 | RDKit::ROMOL_SPTR mol = python::extract(bbs[i][j]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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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-DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/test.cpp.o -MF CMakeFiles/testDescriptors.dir/test.cpp.o.d -o CMakeFiles/testDescriptors.dir/test.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/test.cpp In copy constructor 'boost::shared_ptr::shared_ptr(const boost::shared_ptr&) [with T = RDKit::ROMol]', inlined from 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::list]' at /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:25: /usr/include/boost/smart_ptr/shared_ptr.hpp:459:66: warning: '*(const boost::shared_ptr*)((char*)& + offsetof(boost::python::extract >,boost::python::extract >::.boost::python::converter::extract_rvalue >::m_data.boost::python::converter::rvalue_from_python_data >::.boost::python::converter::rvalue_from_python_storage >::storage)).boost::shared_ptr::px' may be used uninitialized [-Wmaybe-uninitialized] @@ -6688,225 +6545,424 @@ /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:39: note: '' declared here 55 | RDKit::ROMOL_SPTR mol = python::extract(bbs[i][j]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 90%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o -cd 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/usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 88%] Built target testCIPLabeler +make -f Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/DependInfo.cmake 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Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. 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/usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 92%] Built target molStandardizeCatchTest -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMolStandardize.dir/link.d -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 CMakeFiles/rdMolStandardize.dir/Pipeline.cpp.o ../../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 92%] Built target testRDFcustom make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 92%] Built target rdMolStandardize -[ 92%] Linking CXX executable testCIPLabeler -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCIPLabeler.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testCIPLabeler.dir/link.d CMakeFiles/testCIPLabeler.dir/catch_tests.cpp.o CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o CMakeFiles/testCIPLabeler.dir/Node.cpp.o CMakeFiles/testCIPLabeler.dir/Edge.cpp.o CMakeFiles/testCIPLabeler.dir/Sort.cpp.o CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o CMakeFiles/testCIPLabeler.dir/configs/AtropisomerBond.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule1a.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule4b.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule4c.cpp.o 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../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 92%] Built target testMORSE +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testGETAWAY.dir/link.d CMakeFiles/testGETAWAY.dir/testGETAWAY.cpp.o -o testGETAWAY ../../../lib/libRDKitDescriptors.so.1.2025.03.1 ../../../lib/libRDKitPartialCharges.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 92%] Built target testCIPLabeler -[ 92%] Linking CXX shared library ../../../lib/libRDKitGeneralizedSubstruct.so +[ 92%] Built target testGETAWAY +[ 92%] Linking CXX executable testRDF +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRDF.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testRDF.dir/link.d 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/usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 92%] Built target testRDF +[ 92%] Linking CXX executable testAUTOCORR3D +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAUTOCORR3D.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testAUTOCORR3D.dir/link.d CMakeFiles/testAUTOCORR3D.dir/testAUTOCORR3D.cpp.o -o testAUTOCORR3D ../../../lib/libRDKitDescriptors.so.1.2025.03.1 ../../../lib/libRDKitPartialCharges.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 92%] Built target testAUTOCORR3D +[ 92%] Linking CXX executable testCoulombMat +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCoulombMat.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testCoulombMat.dir/link.d CMakeFiles/testCoulombMat.dir/testCoulombMat.cpp.o -o testCoulombMat ../../../lib/libRDKitDescriptors.so.1.2025.03.1 ../../../lib/libRDKitDistGeomHelpers.so.1.2025.03.1 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../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 92%] Built target testCoulombMat +[ 92%] Linking CXX executable moldraw2DTest1 +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DTest1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/moldraw2DTest1.dir/link.d CMakeFiles/moldraw2DTest1.dir/test1.cpp.o -o moldraw2DTest1 ../../../lib/libRDKitMolDraw2D.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libcairo.so /usr/lib/x86_64-linux-gnu/libfreetype.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 92%] Built target moldraw2DTest1 +[ 93%] Linking CXX shared module ../../../rdkit/Chem/rdmolfiles.so +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdmolfiles.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 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../../../lib/libRDKitMarvinParser.so.1.2025.03.1 ../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 -ldl /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 93%] Built target rdmolfiles +[ 93%] Linking CXX executable descriptorsTestCatch +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/descriptorsTestCatch.dir/link.txt --verbose=1 +[ 94%] Linking CXX executable test3D +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/test3D.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/descriptorsTestCatch.dir/link.d CMakeFiles/descriptorsTestCatch.dir/catch_tests.cpp.o -o descriptorsTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitDescriptors.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 94%] Built target descriptorsTestCatch +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/test3D.dir/link.d CMakeFiles/test3D.dir/test3D.cpp.o -o test3D ../../../lib/libRDKitDescriptors.so.1.2025.03.1 ../../../lib/libRDKitPartialCharges.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 94%] Built target test3D +[ 94%] Linking CXX executable testDescriptors +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDescriptors.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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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-Wl,--dependency-file=CMakeFiles/GeneralizedSubstruct.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitGeneralizedSubstruct.so.1 -o ../../../lib/libRDKitGeneralizedSubstruct.so.1.2025.03.1 CMakeFiles/GeneralizedSubstruct.dir/XQMol.cpp.o CMakeFiles/GeneralizedSubstruct.dir/TextIO.cpp.o ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/DependInfo.cmake "--color=" +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-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/DependInfo.cmake "--color=" +make -f Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/build.make Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/GeneralizedSubstruct /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/SynthonSpaceSearch_details.cpp +[ 95%] Building CXX object Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o +[ 95%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpace.cpp.o +[ 95%] Building CXX object Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_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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/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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-202503.1/Code/GraphMol/GeneralizedSubstruct/Wrap/rdGeneralizedSubstruct.cpp +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK 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CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o.d -o CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SubstructLibrary/SubstructLibrary.cpp +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SYNTHONSPACESEARCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings 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/usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/PgSQL/rdkit/CMakeFiles/rdkit.dir/bitstring.c.o -MF CMakeFiles/rdkit.dir/bitstring.c.o.d -o CMakeFiles/rdkit.dir/bitstring.c.o -c /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/bitstring.c -[ 95%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/rdkit_io.c.o -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD 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/build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/rxn_op.c -[ 95%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/sfp_op.c.o +[ 97%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/rdkit_io.c.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2025.03.1\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/PgSQL/rdkit/CMakeFiles/rdkit.dir/rdkit_io.c.o -MF CMakeFiles/rdkit.dir/rdkit_io.c.o.d -o CMakeFiles/rdkit.dir/rdkit_io.c.o -c /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/rdkit_io.c +[ 97%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/sfp_op.c.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc 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-ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/PgSQL/rdkit/CMakeFiles/rdkit.dir/sfp_op.c.o -MF CMakeFiles/rdkit.dir/sfp_op.c.o.d -o CMakeFiles/rdkit.dir/sfp_op.c.o -c /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/sfp_op.c -[ 95%] Linking CXX shared module ../../../../rdkit/Chem/rdMolDescriptors.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolDescriptors.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMolDescriptors.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolDescriptors.so CMakeFiles/rdMolDescriptors.dir/rdMolDescriptors.cpp.o ../../../../lib/libRDKitDescriptors.so.1.2025.03.1 ../../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitPartialCharges.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 97%] Linking CXX shared module ../../../../rdkit/Chem/Draw/rdMolDraw2D.so +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolDraw2D.dir/link.txt --verbose=1 +[ 97%] Linking CXX shared library ../../../lib/libRDKitO3AAlign.so +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/O3AAlign.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMolDraw2D.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/Draw/rdMolDraw2D.so CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o ../../../../lib/libRDKitMolDraw2D.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcairo.so /usr/lib/x86_64-linux-gnu/libfreetype.so /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 95%] Built target rdMolDescriptors -[ 95%] Linking CXX shared module ../../../../rdkit/Chem/rdTautomerQuery.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdTautomerQuery.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdTautomerQuery.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdTautomerQuery.so CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o ../../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 97%] Built target rdMolDraw2D +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/O3AAlign.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitO3AAlign.so.1 -o ../../../lib/libRDKitO3AAlign.so.1.2025.03.1 CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o ../../../lib/libRDKitDescriptors.so.1.2025.03.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../lib/libRDKitPartialCharges.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitO3AAlign.so.1.2025.03.1 ../../../lib/libRDKitO3AAlign.so.1 ../../../lib/libRDKitO3AAlign.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 97%] Built target O3AAlign +make -f Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/depend +make -f Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/build.make Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolAlign/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 95%] Built target rdTautomerQuery +make -f Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/build.make Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 97%] Building CXX object Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o +[ 97%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolAlign_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/Wrap/CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o -MF CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o.d -o CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o -MF CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o.d -o CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolAlign/testO3AAlign.cpp /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/adapter.cpp: In function 'void* makeAvalonBFP(CROMol, bool, unsigned int)': /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/adapter.cpp:1636:38: warning: unused parameter 'data' [-Wunused-parameter] 1636 | extern "C" CBfp makeAvalonBFP(CROMol data, bool isQuery, @@ -6917,22 +6973,12 @@ /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/adapter.cpp:1637:44: warning: unused parameter 'bitFlags' [-Wunused-parameter] 1637 | unsigned int bitFlags) { | ~~~~~~~~~~~~~^~~~~~~~ -[ 96%] Linking CXX shared module ../../../rdkit/Chem/rdmolfiles.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdmolfiles.dir/link.txt --verbose=1 -[ 96%] Linking CXX executable testO3AAlign -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/testO3AAlign.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdmolfiles.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdmolfiles.so CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/MaeWriter.cpp.o CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o ../../../lib/libRDKitMarvinParser.so.1.2025.03.1 ../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 -ldl /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 96%] Built target rdmolfiles -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testO3AAlign.dir/link.d CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o -o testO3AAlign ../../../lib/libRDKitO3AAlign.so.1.2025.03.1 ../../../lib/libRDKitDescriptors.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitDistGeomHelpers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitDistGeometry.so.1.2025.03.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 96%] Built target testO3AAlign -[ 96%] Linking CXX shared library ../../../lib/libRDKitRGroupDecomposition.so +[ 97%] Linking CXX shared library ../../../lib/libRDKitRGroupDecomposition.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/RGroupDecomposition.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/RGroupDecomposition.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRGroupDecomposition.so.1 -o ../../../lib/libRDKitRGroupDecomposition.so.1.2025.03.1 CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupDecompData.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupData.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupDecompJSONParsers.cpp.o ../../../lib/libRDKitFMCS.so.1.2025.03.1 ../../../lib/libRDKitga.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitRGroupDecomposition.so.1.2025.03.1 ../../../lib/libRDKitRGroupDecomposition.so.1 ../../../lib/libRDKitRGroupDecomposition.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 96%] Built target RGroupDecomposition +[ 97%] 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 -f 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-I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o -MF CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o.d -o CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition/catch_rgd.cpp -[ 96%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/gaExample.dir/GaExample.cpp.o +[ 97%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/gaExample.dir/GaExample.cpp.o cd 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-D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/gaExample.dir/GaExample.cpp.o -MF CMakeFiles/gaExample.dir/GaExample.cpp.o.d -o CMakeFiles/gaExample.dir/GaExample.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition/GaExample.cpp -[ 97%] Linking CXX shared module ../../../../rdkit/Chem/Scaffolds/rdScaffoldNetwork.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdScaffoldNetwork.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing 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rdChemReactions +[ 97%] Linking CXX shared module ../../../../rdkit/Chem/rdGeneralizedSubstruct.so +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdGeneralizedSubstruct.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdGeneralizedSubstruct.so CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o ../../../../lib/libRDKitGeneralizedSubstruct.so.1.2025.03.1 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../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 97%] Built target rdGeneralizedSubstruct [ 97%] Linking CXX executable generalizedSubstructCatch cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/generalizedSubstructCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/generalizedSubstructCatch.dir/link.d CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o -o generalizedSubstructCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitGeneralizedSubstruct.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 97%] Built target generalizedSubstructCatch -[ 97%] Linking CXX shared module ../../../../rdkit/Chem/rdMolAlign.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolAlign.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMolAlign.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolAlign.so CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o ../../../../lib/libRDKitO3AAlign.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitDescriptors.so.1.2025.03.1 ../../../../lib/libRDKitPartialCharges.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 97%] Built target rdMolAlign -[ 97%] Linking CXX executable moldraw2DTest1 -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DTest1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/moldraw2DTest1.dir/link.d CMakeFiles/moldraw2DTest1.dir/test1.cpp.o -o moldraw2DTest1 ../../../lib/libRDKitMolDraw2D.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libcairo.so /usr/lib/x86_64-linux-gnu/libfreetype.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 97%] Built target moldraw2DTest1 [ 97%] Linking CXX shared library librdkit.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdkit.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/rdkit.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,librdkit.so -o librdkit.so CMakeFiles/rdkit.dir/adapter.cpp.o CMakeFiles/rdkit.dir/bfp_op.c.o CMakeFiles/rdkit.dir/cache.c.o CMakeFiles/rdkit.dir/guc.c.o CMakeFiles/rdkit.dir/low_gist.c.o CMakeFiles/rdkit.dir/mol_op.c.o CMakeFiles/rdkit.dir/rdkit_gist.c.o CMakeFiles/rdkit.dir/bfp_gist.c.o CMakeFiles/rdkit.dir/bfp_gin.c.o CMakeFiles/rdkit.dir/bitstring.c.o CMakeFiles/rdkit.dir/rdkit_io.c.o CMakeFiles/rdkit.dir/rxn_op.c.o CMakeFiles/rdkit.dir/sfp_op.c.o -L/build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/lib /usr/lib/x86_64-linux-gnu/libpq.so ../../../lib/libRDKitRDInchiLib.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libinchi.so ../../../lib/libRDKitMolInterchange.so.1.2025.03.1 ../../../lib/libRDKitGeneralizedSubstruct.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolDraw2D.so.1.2025.03.1 ../../../lib/libRDKitMolHash.so.1.2025.03.1 ../../../lib/libRDKitFMCS.so.1.2025.03.1 ../../../lib/libRDKitDescriptors.so.1.2025.03.1 ../../../lib/libRDKitPartialCharges.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcairo.so /usr/lib/x86_64-linux-gnu/libfreetype.so ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 -ldl /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 @@ -7011,39 +7052,69 @@ cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cmake -E copy_directory /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/expected /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/PgSQL/rdkit/expected make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 97%] Built target rdkit -[ 97%] Linking CXX shared module ../../../../rdkit/Chem/rdGeneralizedSubstruct.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdGeneralizedSubstruct.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdGeneralizedSubstruct.so CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o ../../../../lib/libRDKitGeneralizedSubstruct.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 97%] Built target rdGeneralizedSubstruct -[ 97%] Linking CXX executable testReaction -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReaction.dir/link.txt --verbose=1 -[ 97%] Linking CXX shared module ../../../rdkit/Chem/rdchem.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdchem.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testReaction.dir/link.d CMakeFiles/testReaction.dir/testReaction.cpp.o -o testReaction ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 97%] Linking CXX executable testO3AAlign +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/testO3AAlign.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testO3AAlign.dir/link.d CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o -o testO3AAlign ../../../lib/libRDKitO3AAlign.so.1.2025.03.1 ../../../lib/libRDKitDescriptors.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitDistGeomHelpers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitDistGeometry.so.1.2025.03.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 97%] Built target testReaction -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdchem.dir/link.d -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.1.2025.03.1 ../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 97%] Built target testO3AAlign +[ 97%] Linking CXX executable gaExample +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/gaExample.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gaExample.dir/link.d CMakeFiles/gaExample.dir/GaExample.cpp.o -o gaExample ../../../lib/libRDKitRGroupDecomposition.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 ../../../lib/libRDKitFMCS.so.1.2025.03.1 ../../../lib/libRDKitga.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 97%] Built target rdchem +[ 97%] Built target gaExample [ 97%] Linking CXX executable testRGroupDecompInternals cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRGroupDecompInternals.dir/link.txt --verbose=1 +[ 97%] Linking CXX shared module ../../../../rdkit/Chem/rdRGroupDecomposition.so +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdRGroupDecomposition.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testRGroupDecompInternals.dir/link.d CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o -o testRGroupDecompInternals ../../../lib/libRDKitRGroupDecomposition.so.1.2025.03.1 ../../../lib/libRDKitFMCS.so.1.2025.03.1 ../../../lib/libRDKitga.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 97%] Built target testRGroupDecompInternals -[ 97%] Linking CXX executable gaExample -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/gaExample.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gaExample.dir/link.d CMakeFiles/gaExample.dir/GaExample.cpp.o -o gaExample ../../../lib/libRDKitRGroupDecomposition.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 ../../../lib/libRDKitFMCS.so.1.2025.03.1 ../../../lib/libRDKitga.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 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/usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdRGroupDecomposition.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdRGroupDecomposition.so CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o ../../../../lib/libRDKitRGroupDecomposition.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitFMCS.so.1.2025.03.1 ../../../../lib/libRDKitga.so.1.2025.03.1 ../../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../../lib/libRDKitCatalogs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 97%] Built target gaExample +[ 97%] Built target rdRGroupDecomposition +[ 97%] Linking CXX shared module ../../../../rdkit/Chem/rdMolDescriptors.so +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolDescriptors.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 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../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 97%] Built target rdMolDescriptors +[ 97%] Linking CXX shared module ../../../../rdkit/Chem/rdMolAlign.so +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolAlign.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMolAlign.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolAlign.so CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o ../../../../lib/libRDKitO3AAlign.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitDescriptors.so.1.2025.03.1 ../../../../lib/libRDKitPartialCharges.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 97%] Built target rdMolAlign +[ 97%] Linking CXX executable rgroupCatchTests +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/rgroupCatchTests.dir/link.d CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o -o rgroupCatchTests ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitRGroupDecomposition.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitFMCS.so.1.2025.03.1 ../../../lib/libRDKitga.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 97%] Built target rgroupCatchTests +[ 97%] Linking CXX shared library ../../../lib/libRDKitSynthonSpaceSearch.so +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/cmake -E cmake_link_script CMakeFiles/SynthonSpaceSearch.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/SynthonSpaceSearch.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSynthonSpaceSearch.so.1 -o ../../../lib/libRDKitSynthonSpaceSearch.so.1.2025.03.1 CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearch_details.cpp.o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpace.cpp.o CMakeFiles/SynthonSpaceSearch.dir/SynthonSet.cpp.o CMakeFiles/SynthonSpaceSearch.dir/Synthon.cpp.o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearcher.cpp.o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSubstructureSearcher.cpp.o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceFingerprintSearcher.cpp.o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceRascalSearcher.cpp.o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceHitSet.cpp.o CMakeFiles/SynthonSpaceSearch.dir/SearchResults.cpp.o CMakeFiles/SynthonSpaceSearch.dir/MemoryMappedFileReader.cpp.o ../../../lib/libRDKitRascalMCES.so.1.2025.03.1 ../../../lib/libRDKitGeneralizedSubstruct.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSynthonSpaceSearch.so.1.2025.03.1 ../../../lib/libRDKitSynthonSpaceSearch.so.1 ../../../lib/libRDKitSynthonSpaceSearch.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 97%] Built target SynthonSpaceSearch +make -f Code/GraphMol/SynthonSpaceSearch/Wrap/CMakeFiles/rdSynthonSpaceSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/Wrap/CMakeFiles/rdSynthonSpaceSearch.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/Wrap/CMakeFiles/rdSynthonSpaceSearch.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/GraphMol/SynthonSpaceSearch/Wrap/CMakeFiles/rdSynthonSpaceSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/Wrap/CMakeFiles/rdSynthonSpaceSearch.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 97%] Building CXX object Code/GraphMol/SynthonSpaceSearch/Wrap/CMakeFiles/rdSynthonSpaceSearch.dir/rdSynthonSpaceSearch.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/SynthonSpaceSearch/Wrap/CMakeFiles/rdSynthonSpaceSearch.dir/rdSynthonSpaceSearch.cpp.o -MF CMakeFiles/rdSynthonSpaceSearch.dir/rdSynthonSpaceSearch.cpp.o.d -o CMakeFiles/rdSynthonSpaceSearch.dir/rdSynthonSpaceSearch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/Wrap/rdSynthonSpaceSearch.cpp [ 97%] Linking CXX shared library ../../../lib/libRDKitSubstructLibrary.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/SubstructLibrary.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/SubstructLibrary.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSubstructLibrary.so.1 -o ../../../lib/libRDKitSubstructLibrary.so.1.2025.03.1 CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o ../../../lib/libRDKitGeneralizedSubstruct.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubstructLibrary.so.1.2025.03.1 ../../../lib/libRDKitSubstructLibrary.so.1 ../../../lib/libRDKitSubstructLibrary.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 97%] Built target SubstructLibrary +make -f Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/depend +make -f Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceRascalSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceRascalSearch.dir/depend make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/DependInfo.cmake "--color=" 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-202503.1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceRascalSearch.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-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/DependInfo.cmake "--color=" @@ -7052,104 +7123,69 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SubstructLibrary/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build -make -f Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceRascalSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceRascalSearch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 97%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -[ 97%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o -[ 97%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -[ 97%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB 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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-202503.1/Code/GraphMol/SubstructLibrary/Wrap/SubstructLibraryWrap.cpp -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code 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-I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o -MF CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o.d -o CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SubstructLibrary/catch_tests.cpp -[ 97%] Linking CXX shared module ../../../../rdkit/Chem/Draw/rdMolDraw2D.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap && /usr/bin/cmake -E cmake_link_script 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/usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 97%] Built target rdMolDraw2D -[ 97%] Linking CXX shared library ../../../lib/libRDKitSynthonSpaceSearch.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/cmake -E cmake_link_script CMakeFiles/SynthonSpaceSearch.dir/link.txt --verbose=1 -[ 97%] Linking CXX executable rgroupCatchTests -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/rgroupCatchTests.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time 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-cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/Wrap/CMakeFiles/rdSynthonSpaceSearch.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' 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Code/GraphMol/SynthonSpaceSearch/Wrap/CMakeFiles/rdSynthonSpaceSearch.dir/rdSynthonSpaceSearch.cpp.o +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 98%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceRascalSearch.dir/rascal_search_catch_tests.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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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Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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../../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../../lib/libRDKitCatalogs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 98%] Built target moldraw2DTestCatch +[ 98%] Linking CXX executable testRGroupDecomp +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRGroupDecomp.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testRGroupDecomp.dir/link.d CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -o testRGroupDecomp ../../../lib/libRDKitRGroupDecomposition.so.1.2025.03.1 ../../../lib/libRDKitFMCS.so.1.2025.03.1 ../../../lib/libRDKitga.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 98%] Built target rdRGroupDecomposition -[ 98%] Linking CXX executable substructLibraryCatchTest -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/substructLibraryCatchTest.dir/link.d CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o -o substructLibraryCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitSubstructLibrary.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitGeneralizedSubstruct.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 98%] Built target testRGroupDecomp +[ 98%] Linking CXX shared module ../../../../rdkit/Chem/rdSynthonSpaceSearch.so +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSynthonSpaceSearch.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdSynthonSpaceSearch.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdSynthonSpaceSearch.so CMakeFiles/rdSynthonSpaceSearch.dir/rdSynthonSpaceSearch.cpp.o ../../../../lib/libRDKitSynthonSpaceSearch.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitRascalMCES.so.1.2025.03.1 ../../../../lib/libRDKitGeneralizedSubstruct.so.1.2025.03.1 ../../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../../lib/libRDKitCatalogs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 98%] Built target substructLibraryCatchTest +[ 98%] Built target rdSynthonSpaceSearch [ 99%] Linking CXX executable substructLibraryTest cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructLibraryTest.dir/link.txt --verbose=1 +[ 99%] Linking CXX executable testSynthonSpaceRascalSearch +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSynthonSpaceRascalSearch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/substructLibraryTest.dir/link.d CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -o substructLibraryTest ../../../lib/libRDKitSubstructLibrary.so.1.2025.03.1 ../../../lib/libRDKitGeneralizedSubstruct.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 99%] Built target substructLibraryTest -[ 99%] Linking CXX executable testSynthonSpaceRascalSearch -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSynthonSpaceRascalSearch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testSynthonSpaceRascalSearch.dir/link.d CMakeFiles/testSynthonSpaceRascalSearch.dir/rascal_search_catch_tests.cpp.o -o testSynthonSpaceRascalSearch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitSubstructLibrary.so.1.2025.03.1 ../../../lib/libRDKitSynthonSpaceSearch.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitGeneralizedSubstruct.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitRascalMCES.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 99%] Built target testSynthonSpaceRascalSearch +[ 99%] Linking CXX executable substructLibraryCatchTest +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/substructLibraryCatchTest.dir/link.d CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o -o substructLibraryCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitSubstructLibrary.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitGeneralizedSubstruct.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 99%] Built target substructLibraryCatchTest [ 99%] Linking CXX executable testSynthonSpaceSubstructureSearch cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSynthonSpaceSubstructureSearch.dir/link.txt --verbose=1 -/usr/bin/ld: [ 99%] Linking CXX executable testRGroupDecomp -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRGroupDecomp.dir/link.txt --verbose=1 -CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o: in function `CATCH2_INTERNAL_TEST_20()': +/usr/bin/ld: CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o: in function `CATCH2_INTERNAL_TEST_20()': ./obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/./Code/GraphMol/SynthonSpaceSearch/substructure_search_catch_tests.cpp:334:(.text+0x1866): warning: the use of `tmpnam' is dangerous, better use `mkstemp' -[ 99%] Linking CXX shared module ../../../../rdkit/Chem/rdSynthonSpaceSearch.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSynthonSpaceSearch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testSynthonSpaceSubstructureSearch.dir/link.d CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o -o testSynthonSpaceSubstructureSearch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitSubstructLibrary.so.1.2025.03.1 ../../../lib/libRDKitSynthonSpaceSearch.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitGeneralizedSubstruct.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitRascalMCES.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 99%] Built target testSynthonSpaceSubstructureSearch -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testRGroupDecomp.dir/link.d CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -o testRGroupDecomp ../../../lib/libRDKitRGroupDecomposition.so.1.2025.03.1 ../../../lib/libRDKitFMCS.so.1.2025.03.1 ../../../lib/libRDKitga.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 99%] Built target testRGroupDecomp -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdSynthonSpaceSearch.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdSynthonSpaceSearch.so CMakeFiles/rdSynthonSpaceSearch.dir/rdSynthonSpaceSearch.cpp.o ../../../../lib/libRDKitSynthonSpaceSearch.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitRascalMCES.so.1.2025.03.1 ../../../../lib/libRDKitGeneralizedSubstruct.so.1.2025.03.1 ../../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../../lib/libRDKitCatalogs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 99%] Built target rdSynthonSpaceSearch -[ 99%] Linking CXX executable moldraw2DTestCatch -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DTestCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/moldraw2DTestCatch.dir/link.d CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -o moldraw2DTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolDraw2D.so.1.2025.03.1 ../../../lib/libRDKitCIPLabeler.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 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/usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 99%] Built target moldraw2DTestCatch [100%] Linking CXX shared module ../../../../rdkit/Chem/rdSubstructLibrary.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSubstructLibrary.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdSubstructLibrary.dir/link.d -Wl,-z,relro 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../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl @@ -7281,77 +7317,77 @@ Searching for files to exclude Searching INPUT for files to process... 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/FragmentCatalog Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/TransformCatalog -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/Fonts -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/Qt -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/Qt/Demo -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/libs -Searching for files in directory 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Trajectory -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/data -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/TautomerQuery -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/MMFF -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/CrystalFF -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/UFF -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SubstructLibrary -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Enumerate -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/tutorial -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInteractionFields -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/GenericGroups -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/DistGeomHelpers Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolChemicalFeatures +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Deprotect Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/DetermineBonds -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/Test -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInterchange -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ScaffoldNetwork -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/Qt +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/Qt/Demo +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/Fonts +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInteractionFields +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/PartialCharges +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolProcessing Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/StructChecker -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ReducedGraphs -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SLNParse +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Depictor +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemTransforms +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MarvinParse +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/data +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ShapeHelpers +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/libs Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/Catalogs Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/DataStructs Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/Query Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/ML -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/ML/Data -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/ML/InfoTheory Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/ML/Cluster Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/ML/Cluster/Murtagh +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/ML/InfoTheory +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/ML/Data Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/DataManip Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/DataManip/MetricMatrixCalc Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/SimDivPickers @@ -7361,12 +7397,12 @@ Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/RDBoost Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/DistGeom Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/ForceField -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/ForceField/UFF +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/Numerics -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/Numerics/Alignment -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/Numerics/Optimizer Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/Numerics/EigenSolvers +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/Numerics/Optimizer +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/Numerics/Alignment Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/Geometry Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/Features Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/ChemicalFeatures @@ -8389,6 +8425,11 @@ Generating code for file Contrib.h... Generating code for file DistanceConstraints.h... Generating code for file ForceField.h... +Generating code for file OopBend.h... +Generating code for file StretchBend.h... +Generating code for file TorsionConstraint.h... +Generating code for file TorsionConstraint.h... +Generating code for file TorsionConstraint.h... Generating code for file AngleBend.h... Generating code for file AngleBend.h... Generating code for file AngleConstraint.h... @@ -8401,22 +8442,17 @@ Generating code for file DistanceConstraint.h... Generating code for file DistanceConstraint.h... Generating code for file DistanceConstraint.h... +Generating code for file Inversion.h... +Generating code for file Inversions.h... Generating code for file Nonbonded.h... Generating code for file Nonbonded.h... -Generating code for file OopBend.h... Generating code for file Params.h... Generating code for file Params.h... Generating code for file PositionConstraint.h... Generating code for file PositionConstraint.h... Generating code for file PositionConstraint.h... -Generating code for file StretchBend.h... Generating code for file TorsionAngle.h... Generating code for file TorsionAngle.h... -Generating code for file TorsionConstraint.h... -Generating code for file TorsionConstraint.h... -Generating code for file TorsionConstraint.h... -Generating code for file Inversion.h... -Generating code for file Inversions.h... Generating code for file Utils.h... Generating code for file Utils.h... Generating code for file Grid3D.h... @@ -8516,8 +8552,6 @@ Generating code for file RegisterDescriptor.h... Generating code for file USRDescriptor.h... Generating code for file WHIM.h... -Generating code for file details.h... -Generating code for file details.h... Generating code for file DetermineBonds.h... Generating code for file BoundsMatrixBuilder.h... Generating code for file Embedder.h... @@ -8574,11 +8608,11 @@ Generating code for file TorsionAngleM6.h... Generating code for file TorsionPreferences.h... Generating code for file FFConvenience.h... +Generating code for file MMFF.h... Generating code for file AtomTyper.h... Generating code for file AtomTyper.h... Generating code for file Builder.h... Generating code for file Builder.h... -Generating code for file MMFF.h... Generating code for file UFF.h... Generating code for file FragCatalogEntry.h... Generating code for file FragCatalogUtils.h... @@ -8637,6 +8671,8 @@ Generating code for file MolHash.h... Generating code for file nmmolhash.h... Generating code for file MIFDescriptors.h... +Generating code for file details.h... +Generating code for file details.h... Generating code for file MolInterchange.h... Generating code for file MolOps.h... Generating code for file MolPickler.h... @@ -8839,6 +8875,11 @@ Generating docs for file Contrib.h... Generating docs for file DistanceConstraints.h... Generating docs for file ForceField.h... +Generating docs for file OopBend.h... +Generating docs for file StretchBend.h... +Generating docs for file TorsionConstraint.h... +Generating docs for file TorsionConstraint.h... +Generating docs for file TorsionConstraint.h... Generating docs for file AngleBend.h... Generating docs for file AngleBend.h... Generating docs for file AngleConstraint.h... @@ -8851,22 +8892,17 @@ Generating docs for file DistanceConstraint.h... Generating docs for file DistanceConstraint.h... Generating docs for file DistanceConstraint.h... +Generating docs for file Inversion.h... +Generating docs for file Inversions.h... Generating docs for file Nonbonded.h... Generating docs for file Nonbonded.h... -Generating docs for file OopBend.h... Generating docs for file Params.h... Generating docs for file Params.h... Generating docs for file PositionConstraint.h... Generating docs for file PositionConstraint.h... Generating docs for file PositionConstraint.h... -Generating docs for file StretchBend.h... Generating docs for file TorsionAngle.h... Generating docs for file TorsionAngle.h... -Generating docs for file TorsionConstraint.h... -Generating docs for file TorsionConstraint.h... -Generating docs for file TorsionConstraint.h... -Generating docs for file Inversion.h... -Generating docs for file Inversions.h... Generating docs for file Utils.h... Generating docs for file Utils.h... Generating docs for file Grid3D.h... @@ -8966,8 +9002,6 @@ Generating docs for file RegisterDescriptor.h... Generating docs for file USRDescriptor.h... Generating docs for file WHIM.h... -Generating docs for file details.h... -Generating docs for file details.h... Generating docs for file DetermineBonds.h... Generating docs for file BoundsMatrixBuilder.h... Generating docs for file Embedder.h... @@ -9024,11 +9058,11 @@ Generating docs for file TorsionAngleM6.h... Generating docs for file TorsionPreferences.h... Generating docs for file FFConvenience.h... +Generating docs for file MMFF.h... Generating docs for file AtomTyper.h... Generating docs for file AtomTyper.h... Generating docs for file Builder.h... Generating docs for file Builder.h... -Generating docs for file MMFF.h... Generating docs for file UFF.h... Generating docs for file FragCatalogEntry.h... Generating docs for file FragCatalogUtils.h... @@ -9060,11 +9094,11 @@ Generating docs for file DrawShape.h... Generating docs for file DrawText.h... Generating docs for file DrawTextCairo.h... -Generating docs for file DrawTextFT./build/reproducible-path/rdkit-202503.1/Code/GraphMol/QueryOps.h:526: warning: Found unknown command '\overloadquery' -/build/reproducible-path/rdkit-202503.1/Code/GraphMol/QueryOps.h:535: warning: Found unknown command '\overloadquery' -h... +Generating docs for file DrawTextFT.h... Generating docs for file DrawTextFTCairo.h... -Generating docs for file DrawTextFTJS.h... +Generating docs for file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/QueryOps.h:526: warning: Found unknown command '\overloadquery' +/build/reproducible-path/rdkit-202503.1/Code/GraphMol/QueryOps.h:535: warning: Found unknown command '\overloadquery' +DrawTextFTJS.h... Generating docs for file DrawTextFTSVG.h... Generating docs for file DrawTextJS.h... Generating docs for file DrawTextNotFT.h... @@ -9089,6 +9123,8 @@ Generating docs for file MolHash.h... Generating docs for file nmmolhash.h... Generating docs for file MIFDescriptors.h... +Generating docs for file details.h... +Generating docs for file details.h... Generating docs for file MolInterchange.h... Generating docs for file MolOps.h... Generating docs for file MolPickler.h... @@ -11259,9 +11295,9 @@ copying downloadable files... [100%] C++Examples/example16.cpp copying static files... -Writing evaluated template result to /build/reproducible-path/rdkit-202503.1/Docs/Book/_build/html/_static/documentation_options.js Writing evaluated template result to /build/reproducible-path/rdkit-202503.1/Docs/Book/_build/html/_static/language_data.js Writing evaluated template result to /build/reproducible-path/rdkit-202503.1/Docs/Book/_build/html/_static/basic.css +Writing evaluated template result to /build/reproducible-path/rdkit-202503.1/Docs/Book/_build/html/_static/documentation_options.js Writing evaluated template result to /build/reproducible-path/rdkit-202503.1/Docs/Book/_build/html/_static/sphinxdoc.css copying static files: done copying extra files... @@ -12547,10 +12583,10 @@ done preparing documents... done copying assets... -copying TeX support files... Writing evaluated template result to /build/reproducible-path/rdkit-202503.1/Docs/Book/_build/latex/Makefile -Writing evaluated template result to /build/reproducible-path/rdkit-202503.1/Docs/Book/_build/latex/latexmkjarc +copying TeX support files... Writing evaluated template result to /build/reproducible-path/rdkit-202503.1/Docs/Book/_build/latex/make.bat +Writing evaluated template result to /build/reproducible-path/rdkit-202503.1/Docs/Book/_build/latex/Makefile Writing evaluated template result to /build/reproducible-path/rdkit-202503.1/Docs/Book/_build/latex/latexmkrc -Writing evaluated template result to /build/reproducible-path/rdkit-202503.1/Docs/Book/_build/latex/make.bat +Writing evaluated template result to /build/reproducible-path/rdkit-202503.1/Docs/Book/_build/latex/latexmkjarc done copying assets: done processing RDKit.tex... @@ -12818,7 +12854,7 @@ resolving references... /build/reproducible-path/rdkit-202503.1/Docs/Book/GettingStartedWithContributing.md:273: WARNING: 'myst' cross-reference target not found: 'building-rdkit-for-development' [myst.xref_missing] -WARNING: Could not fetch remote image: https://img.shields.io/badge/Powered%20by-RDKit-3838ff.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQBAMAAADt3eJSAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAAFVBMVEXc3NwUFP8UPP9kZP+MjP+0tP////9ZXZotAAAAAXRSTlMAQObYZgAAAAFiS0dEBmFmuH0AAAAHdElNRQfmAwsPGi+MyC9RAAAAQElEQVQI12NgQABGQUEBMENISUkRLKBsbGwEEhIyBgJFsICLC0iIUdnExcUZwnANQWfApKCK4doRBsKtQFgKAQC5Ww1JEHSEkAAAACV0RVh0ZGF0ZTpjcmVhdGUAMjAyMi0wMy0xMVQxNToyNjo0NyswMDowMDzr2J4AAAAldEVYdGRhdGU6bW9kaWZ5ADIwMjItMDMtMTFUMTU6MjY6NDcrMDA6MDBNtmAiAAAAAElFTkSuQmCC [HTTPSConnectionPool(host='img.shields.io', port=443): Max retries exceeded with url: /badge/Powered%20by-RDKit-3838ff.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQBAMAAADt3eJSAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAAFVBMVEXc3NwUFP8UPP9kZP+MjP+0tP////9ZXZotAAAAAXRSTlMAQObYZgAAAAFiS0dEBmFmuH0AAAAHdElNRQfmAwsPGi+MyC9RAAAAQElEQVQI12NgQABGQUEBMENISUkRLKBsbGwEEhIyBgJFsICLC0iIUdnExcUZwnANQWfApKCK4doRBsKtQFgKAQC5Ww1JEHSEkAAAACV0RVh0ZGF0ZTpjcmVhdGUAMjAyMi0wMy0xMVQxNToyNjo0NyswMDowMDzr2J4AAAAldEVYdGRhdGU6bW9kaWZ5ADIwMjItMDMtMTFUMTU6MjY6NDcrMDA6MDBNtmAiAAAAAElFTkSuQmCC (Caused by NameResolutionError(": Failed to resolve 'img.shields.io' ([Errno -3] Temporary failure in name resolution)"))] +WARNING: Could not fetch remote image: https://img.shields.io/badge/Powered%20by-RDKit-3838ff.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQBAMAAADt3eJSAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAAFVBMVEXc3NwUFP8UPP9kZP+MjP+0tP////9ZXZotAAAAAXRSTlMAQObYZgAAAAFiS0dEBmFmuH0AAAAHdElNRQfmAwsPGi+MyC9RAAAAQElEQVQI12NgQABGQUEBMENISUkRLKBsbGwEEhIyBgJFsICLC0iIUdnExcUZwnANQWfApKCK4doRBsKtQFgKAQC5Ww1JEHSEkAAAACV0RVh0ZGF0ZTpjcmVhdGUAMjAyMi0wMy0xMVQxNToyNjo0NyswMDowMDzr2J4AAAAldEVYdGRhdGU6bW9kaWZ5ADIwMjItMDMtMTFUMTU6MjY6NDcrMDA6MDBNtmAiAAAAAElFTkSuQmCC [HTTPSConnectionPool(host='img.shields.io', port=443): Max retries exceeded with url: /badge/Powered%20by-RDKit-3838ff.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQBAMAAADt3eJSAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAAFVBMVEXc3NwUFP8UPP9kZP+MjP+0tP////9ZXZotAAAAAXRSTlMAQObYZgAAAAFiS0dEBmFmuH0AAAAHdElNRQfmAwsPGi+MyC9RAAAAQElEQVQI12NgQABGQUEBMENISUkRLKBsbGwEEhIyBgJFsICLC0iIUdnExcUZwnANQWfApKCK4doRBsKtQFgKAQC5Ww1JEHSEkAAAACV0RVh0ZGF0ZTpjcmVhdGUAMjAyMi0wMy0xMVQxNToyNjo0NyswMDowMDzr2J4AAAAldEVYdGRhdGU6bW9kaWZ5ADIwMjItMDMtMTFUMTU6MjY6NDcrMDA6MDBNtmAiAAAAAElFTkSuQmCC (Caused by NameResolutionError(": Failed to resolve 'img.shields.io' ([Errno -3] Temporary failure in name resolution)"))] processing RDKit.tex: done writing... done copying images... [ 1%] images/Cc1ccccc1.png @@ -14946,10 +14982,10 @@ find /build/reproducible-path/rdkit-202503.1 -name rdchem.so /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so PYTHONPATH=/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/:/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//rdkit/Chem/ LD_LIBRARY_PATH="/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib:" dh_auto_test - cd obj-x86_64-linux-gnu && make -j42 test ARGS\+=--verbose ARGS\+=-j42 + cd obj-x86_64-linux-gnu && make -j40 test ARGS\+=--verbose ARGS\+=-j40 make[2]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' Running tests... -/usr/bin/ctest --force-new-ctest-process --verbose -j42 +/usr/bin/ctest --force-new-ctest-process --verbose -j40 UpdateCTestConfiguration from :/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/DartConfiguration.tcl Parse Config file:/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/DartConfiguration.tcl Add coverage exclude regular expressions. @@ -15203,18 +15239,6 @@ 40: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/hanoiTest 40: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol 40: Test timeout computed to be: 1500 -test 41 - Start 41: graphmolMemTest1 - -41: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolMemTest1 -41: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol -41: Test timeout computed to be: 1500 -test 42 - Start 42: resMolSupplierTest - -42: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/resMolSupplierTest -42: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol -42: Test timeout computed to be: 1500 1: core 1: RDKit 2D 1: @@ -15672,41 +15696,401 @@ 1: 2 5 1 0 1: M END 1: -3: [17:55:16] Testing Github940: property dictionaries leaking memory -3: [17:55:16] done +1: cyclosporine a +1: RDKit 2D +1: +1: 85 85 0 0 0 0 0 0 0 0999 V2000 +1: 1.4840 -0.8529 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 0.6174 -1.3521 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 0.6176 -2.3509 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 1.4860 -2.8479 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 1.4912 -3.8491 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +1: 2.3504 -2.3385 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 +1: 2.3352 -1.3311 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 3.1902 -0.7993 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 3.1580 0.1961 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +1: 4.0642 -1.2607 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 +1: 4.9260 -0.7295 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 4.9144 0.3303 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 5.7766 0.8337 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +1: 4.0008 0.8409 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 +1: 3.8596 1.9125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 2.8162 2.2071 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 2.2038 1.4219 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +1: 2.2560 3.1855 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 +1: 2.5280 4.2325 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 1.7128 4.8927 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 1.8530 5.8895 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +1: 0.7676 4.5077 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 +1: -0.0820 5.0835 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -0.9744 4.6151 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -1.8344 5.1337 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +1: -0.9792 3.6203 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 +1: -1.8192 3.0813 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -2.7974 3.5817 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -2.7998 4.5809 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +1: -3.7790 3.0789 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 +1: -3.8812 2.0705 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -3.1202 1.6015 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -2.4194 2.0931 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +1: -3.0590 0.6211 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 +1: -3.8626 0.0983 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -3.8096 -0.8961 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -4.6470 -1.4375 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +1: -2.9122 -1.3587 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 +1: -2.8776 -2.3565 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -1.9982 -2.8425 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -1.1382 -2.3311 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +1: -1.9886 -3.8459 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 +1: -1.1202 -4.3461 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -0.2526 -3.8491 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 0.6116 -4.3521 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +1: -0.2494 -2.8505 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 +1: -1.1228 -5.3475 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -0.2584 -5.8507 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 0.6092 -5.3541 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -0.2624 -6.8511 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 0.6018 -7.3547 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 0.5982 -8.3547 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 1.4624 -8.8579 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -1.9906 -5.8449 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +1: -2.8520 -4.3501 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -3.7288 -2.8719 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -3.7098 -3.8701 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -4.6032 -2.3871 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -2.0646 -0.8235 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -4.7362 0.5679 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -5.5794 0.0605 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -5.5618 -0.9361 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -6.4498 0.5487 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -2.1628 0.1727 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -4.7698 1.6253 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -5.5952 2.1745 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -6.4896 1.7311 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -5.5292 3.1711 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -4.6054 3.6407 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -1.7186 2.0867 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -0.0328 6.0847 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 3.4396 4.6417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 3.4580 5.6909 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 4.3220 6.1985 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 2.5836 6.2065 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 1.2682 3.0557 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 4.6630 2.5215 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 5.5876 2.1073 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 4.5648 3.5065 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 5.7968 -1.2481 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 6.6786 -0.7913 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 7.5218 -1.3355 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 6.7252 0.2017 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 4.0970 -2.2659 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 3.2220 -2.8307 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 1 2 1 0 +1: 3 2 1 1 +1: 3 4 1 0 +1: 4 5 2 0 +1: 4 6 1 0 +1: 6 7 1 0 +1: 7 8 1 0 +1: 8 9 2 0 +1: 8 10 1 0 +1: 10 11 1 0 +1: 11 12 1 0 +1: 12 13 2 0 +1: 12 14 1 0 +1: 14 15 1 0 +1: 15 16 1 0 +1: 16 17 2 0 +1: 16 18 1 0 +1: 18 19 1 0 +1: 19 20 1 0 +1: 20 21 2 0 +1: 20 22 1 0 +1: 22 23 1 0 +1: 23 24 1 0 +1: 24 25 2 0 +1: 24 26 1 0 +1: 26 27 1 0 +1: 27 28 1 0 +1: 28 29 2 0 +1: 28 30 1 0 +1: 30 31 1 0 +1: 31 32 1 0 +1: 32 33 2 0 +1: 32 34 1 0 +1: 34 35 1 0 +1: 35 36 1 0 +1: 36 37 2 0 +1: 36 38 1 0 +1: 38 39 1 0 +1: 39 40 1 0 +1: 40 41 2 0 +1: 40 42 1 0 +1: 43 42 1 6 +1: 43 44 1 0 +1: 44 45 2 0 +1: 44 46 1 0 +1: 43 47 1 0 +1: 47 48 1 0 +1: 48 49 1 6 +1: 48 50 1 0 +1: 50 51 1 0 +1: 51 52 2 0 +1: 52 53 1 0 +1: 47 54 1 1 +1: 42 55 1 0 +1: 39 56 1 6 +1: 56 57 1 0 +1: 56 58 1 0 +1: 38 59 1 0 +1: 35 60 1 6 +1: 60 61 1 0 +1: 61 62 1 0 +1: 61 63 1 0 +1: 34 64 1 0 +1: 31 65 1 6 +1: 65 66 1 0 +1: 66 67 1 0 +1: 66 68 1 0 +1: 30 69 1 0 +1: 27 70 1 6 +1: 23 71 1 6 +1: 19 72 1 6 +1: 72 73 1 0 +1: 73 74 1 0 +1: 73 75 1 0 +1: 18 76 1 0 +1: 15 77 1 6 +1: 77 78 1 0 +1: 77 79 1 0 +1: 11 80 1 6 +1: 80 81 1 0 +1: 81 82 1 0 +1: 81 83 1 0 +1: 10 84 1 0 +1: 6 85 1 0 +1: 46 3 1 0 +1: M END +1: +1: single-double +1: RDKit 2D +1: +1: 17 16 0 0 0 0 0 0 0 0999 V2000 +1: -6.9282 -0.2298 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -6.0618 0.2696 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -5.1962 -0.2312 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -4.3298 0.2682 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 +1: -3.4642 -0.2326 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -2.5978 0.2668 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -1.7322 -0.2340 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 +1: -0.8658 0.2654 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -0.0002 -0.2352 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +1: 0.8662 0.2640 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 1.7318 -0.2366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 2.5982 0.2626 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 3.4638 -0.2380 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 4.3302 0.2612 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 5.1958 -0.2394 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 6.0622 0.2598 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +1: 6.9278 -0.2408 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 1 2 1 0 +1: 2 3 1 0 +1: 3 4 1 0 +1: 4 5 1 0 +1: 5 6 2 3 +1: 6 7 1 0 +1: 7 8 1 0 +1: 8 9 1 0 +1: 9 10 1 0 +1: 10 11 2 3 +1: 11 12 1 0 +1: 12 13 2 3 +1: 13 14 1 0 +1: 14 15 2 3 +1: 15 16 1 0 +1: 16 17 1 0 +1: M END +1: +1: cis-trans +1: RDKit 2D +1: +1: 10 9 0 0 0 0 0 0 0 0999 V2000 +1: -3.6370 -0.2028 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +1: -2.7706 -0.7022 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -1.9050 -0.2016 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -1.0386 -0.7008 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -0.1730 -0.2002 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 0.6934 -0.6994 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 1.5590 -0.1988 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 1.5582 0.8012 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 2.4238 1.3020 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 3.2902 0.8026 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 +1: 1 2 1 0 +1: 2 3 2 0 +1: 3 4 1 0 +1: 4 5 2 0 +1: 5 6 1 0 +1: 6 7 2 0 +1: 7 8 1 0 +1: 8 9 2 0 +1: 9 10 1 0 +1: M END +1: +1: admntn +1: RDKit 2D +1: +1: 10 12 0 0 0 0 0 0 0 0999 V2000 +1: 1.3505 -0.5360 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 0.5267 -1.1020 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -0.4629 -1.0366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -0.7523 0.0052 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -1.4741 0.5660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -0.4761 0.5032 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 0.3505 1.0730 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 1.0611 0.5080 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 0.0643 0.5686 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -0.1877 -0.5490 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 1 2 1 0 +1: 2 3 1 0 +1: 3 4 1 0 +1: 4 5 1 0 +1: 5 6 1 0 +1: 6 7 1 0 +1: 7 8 1 0 +1: 8 9 1 0 +1: 6 10 1 0 +1: 8 1 1 0 +1: 9 4 1 0 +1: 10 2 1 0 +1: M END +1: +1: github 4845 - nan coordinates but no crash +1: RDKit 2D +1: +1: 42 44 0 0 0 0 0 0 0 0999 V2000 +1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan O 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan O 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 +1: 1 2 1 0 +1: 2 3 1 0 +1: 2 4 2 0 +1: 4 5 1 0 +1: 5 6 3 0 +1: 6 7 1 0 +1: 7 8 2 0 +1: 8 9 1 0 +1: 9 10 3 0 +1: 10 11 1 0 +1: 11 12 2 0 +1: 12 13 1 0 +1: 13 14 3 0 +1: 14 15 1 0 +1: 15 16 2 0 +1: 16 17 1 0 +1: 16 18 1 0 +1: 12 19 1 0 +1: 19 20 2 0 +1: 20 21 1 0 +1: 20 22 1 0 +1: 19 23 1 0 +1: 23 24 3 0 +1: 24 25 1 0 +1: 25 26 1 0 +1: 26 27 2 0 +1: 27 28 2 0 +1: 26 29 1 0 +1: 29 30 3 0 +1: 8 31 1 0 +1: 31 32 2 0 +1: 32 33 1 0 +1: 32 34 1 0 +1: 31 35 1 0 +1: 35 36 3 0 +1: 36 37 1 0 +1: 37 38 2 0 +1: 37 39 1 0 +1: 39 40 2 0 +1: 40 41 1 0 +1: 40 42 1 0 +1: 39 4 1 0 +1: 15 7 1 0 +1: 30 11 1 0 +1: M END +1: +3: [14:17:36] Testing Github940: property dictionaries leaking memory +3: [14:17:36] done 3: Testing RDValue 3: Testing RDAny 3: dict set int vect 3: dict get int vect -3: static boost any:0.000294 s -3: dynamic boost any:0.001002 s -3: static RDAny:0.000198 s -3: dynamic RDAny:0.000887 s +3: static boost any:0.000538 s +3: dynamic boost any:0.00265 s +3: static RDAny:0.000225 s +3: dynamic RDAny:0.001676 s 3: static RDValue:1e-06 s -3: dynamic RDValue:0.000161 s +3: dynamic RDValue:0.000322 s 3: deleted! -3: [17:55:16] ------------------------------------- -3: [17:55:16] Testing String Pickle Roundtrips. -3: [17:55:16] done -3: [17:55:16] ------------------------------------- -3: [17:55:16] Testing conversion of vect to string. -3: [17:55:16] done -3: [17:55:16] ------------------------------------- -3: [17:55:16] Testing returning const references. -3: [17:55:16] any cast -3: [17:55:16] done: 0.000884 300000 -3: [17:55:16] copy -3: [17:55:16] done: 0.000692 300000 -3: [17:55:16] ref -3: [17:55:16] done: 0.000817 300000 -3: [17:55:16] dict -3: [17:55:16] done: 0.001649 300000 -3: [17:55:16] ref with hasVal -3: [17:55:16] done: 0.001405 300000 -3: [17:55:16] done -3: [17:55:16] ------------------------------------- -3: [17:55:16] Testing dict update. -3: [17:55:16] done +3: [14:17:36] ------------------------------------- +3: [14:17:36] Testing String Pickle Roundtrips. +3: [14:17:36] done +3: [14:17:36] ------------------------------------- +3: [14:17:36] Testing conversion of vect to string. +3: [14:17:36] done +3: [14:17:36] ------------------------------------- +3: [14:17:36] Testing returning const references. +3: [14:17:36] any cast +3: [14:17:36] done: 0.001326 300000 +3: [14:17:36] copy +3: [14:17:36] done: 0.001393 300000 +3: [14:17:36] ref +3: [14:17:36] done: 0.001327 300000 +3: [14:17:36] dict +3: [14:17:36] done: 0.003112 300000 +3: [14:17:36] ref with hasVal +3: [14:17:36] done: 0.002089 300000 +3: [14:17:36] done +3: [14:17:36] ------------------------------------- +3: [14:17:36] Testing dict update. +3: [14:17:36] done 3: deleted! 3: deleted! 3: deleted! @@ -15725,48 +16109,48 @@ 4: == unsigned int 4: == bool 4: == std::string -5: [17:55:16] +5: [14:17:36] 5: ----------------------------------------- -5: [17:55:16] Finished: testPushAndPop() -5: [17:55:16] +5: [14:17:36] Finished: testPushAndPop() +5: [14:17:36] 5: ----------------------------------------- -5: [17:55:16] +5: [14:17:36] 5: ----------------------------------------- -6: Randomness seeded to: 1272285494 +6: Randomness seeded to: 500415071 6: =============================================================================== 6: All tests passed (32 assertions in 2 test cases) 6: -7: [17:55:16] should not be silent -7: [17:55:16] should not be silent -7: Randomness seeded to: 3474013203 -7: [17:55:16] should not be silent -7: [17:55:16] should not be silent -7: [17:55:16] should not be silent -7: [17:55:16] should not be silent -7: [17:55:16] should not be silent -7: [17:55:16] should not be silent -7: [17:55:16] should not be silent -7: [17:55:16] should not be silent +7: [14:17:36] should not be silent +7: [14:17:36] should not be silent +7: Randomness seeded to: 3612450437 +7: [14:17:36] should not be silent +7: [14:17:36] should not be silent +7: [14:17:36] should not be silent +7: [14:17:36] should not be silent +7: [14:17:36] should not be silent +7: [14:17:36] should not be silent +7: [14:17:36] should not be silent +7: [14:17:36] should not be silent 7: =============================================================================== 7: All tests passed (26 assertions in 3 test cases) 7: -8: [17:55:16] pass -8: [17:55:16] v3 4 -8: [17:55:16] v4 5 -8: [17:55:16] SPARSE ----------------------------------- -8: [17:55:16] Set 10: 0 -8: [17:55:16] Set 11: 0 -8: [17:55:16] Set 14: 0 -8: [17:55:16] Set 10: 1 -8: [17:55:16] Get 14: 1 -8: [17:55:16] Num: 20 -8: [17:55:16] NumOn: 3 -8: [17:55:16] NumOff: 17 +8: [14:17:36] pass +8: [14:17:36] v3 4 +8: [14:17:36] v4 5 +8: [14:17:36] SPARSE ----------------------------------- +8: [14:17:36] Set 10: 0 +8: [14:17:36] Set 11: 0 +8: [14:17:36] Set 14: 0 +8: [14:17:36] Set 10: 1 +8: [14:17:36] Get 14: 1 +8: [14:17:36] Num: 20 +8: [14:17:36] NumOn: 3 +8: [14:17:36] NumOff: 17 8: 10, 11, 14, -8: [17:55:16] t2[19]: 0 -8: [17:55:16] t2[14]: 1 -8: [17:55:16] t2[19]: 0 -8: [17:55:16] t2[14]: 0 +8: [14:17:36] t2[19]: 0 +8: [14:17:36] t2[14]: 1 +8: [14:17:36] t2[19]: 0 +8: [14:17:36] t2[14]: 0 8: t1: 10, 11, 14, 8: t2: 10, 11, 15, 17, 8: t1|t2: 10, 11, 14, 15, 17, @@ -15774,20 +16158,20 @@ 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 -8: [17:55:16] Explicit ---------------------------------- -8: [17:55:16] Set 10: 0 -8: [17:55:16] Set 11: 0 -8: [17:55:16] Set 14: 0 -8: [17:55:16] Set 10: 1 -8: [17:55:16] Get 14: 1 -8: [17:55:16] Num: 20 -8: [17:55:16] NumOn: 3 -8: [17:55:16] NumOff: 17 +8: [14:17:36] Explicit ---------------------------------- +8: [14:17:36] Set 10: 0 +8: [14:17:36] Set 11: 0 +8: [14:17:36] Set 14: 0 +8: [14:17:36] Set 10: 1 +8: [14:17:36] Get 14: 1 +8: [14:17:36] Num: 20 +8: [14:17:36] NumOn: 3 +8: [14:17:36] NumOff: 17 8: 10, 11, 14, -8: [17:55:16] t2[19]: 0 -8: [17:55:16] t2[14]: 1 -8: [17:55:16] t2[19]: 0 -8: [17:55:16] t2[14]: 0 +8: [14:17:36] t2[19]: 0 +8: [14:17:36] t2[14]: 1 +8: [14:17:36] t2[19]: 0 +8: [14:17:36] t2[14]: 0 8: t1: 10, 11, 14, 8: t2: 10, 11, 15, 17, 8: t1|t2: 10, 11, 14, 15, 17, @@ -15795,34 +16179,34 @@ 8: t1^t2: 14, 15, 17, 8: ~t1: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 13, 15, 16, 17, 18, 19, 8: except -8: [17:55:16] Done -8: [17:55:16] Test DiscreteValue Vectors 1 ---------------------------- -8: [17:55:16] Expected failure: Value out of range -8: [17:55:16] Expected failure: Value out of range -8: [17:55:16] Expected failure: Value out of range -8: [17:55:16] Expected failure: Value out of range -8: [17:55:16] Expected failure: Value out of range -8: [17:55:16] Test DiscreteValue Vectors 2 ------------------------------ -8: [17:55:16] Test DiscreteValue Vectors 3 --------------------------- -8: [17:55:16] Test DiscreteValue Operations ----------------------------- -8: [17:55:16] Test DiscreteValue Operations 2 -------------------------- -8: [17:55:16] Test SparseIntVect ------------------------------------ -8: [17:55:16] Test SparseIntVect Serialization -------------------------- -8: [17:55:16] Test BitVect Serialization ------------------------------- -8: [17:55:16] Test BitVect to FPS ------------------------------- -8: [17:55:16] Test BitVect to binary string ------------------------------- -8: [17:55:16] Test Similarity Measures BitVect ------------------------------- -8: [17:55:16] Test Similarity Measures SparseBitVect ------------------------------- -8: [17:55:16] Test BitVect with all ones ------------------------------- -8: [17:55:16] Test Explicit BitVects: Concatenation Operation ------------------------------- -8: [17:55:16] Test bitmap operations ------------------------------- -8: [17:55:16] Test bitmaps as properties ------------------------------- -8: [17:55:16] Test #3944: SparseIntVect copy constructor and assignment operators not clearing existing data------------------------------- -8: [17:55:16] Test RealValue Vectors 1: Constructors and Accessing Values ------------------------------- -8: [17:55:16] Test RealValue Vectors 2: L1Norm ------------------------------- -8: [17:55:16] Test RealValue Vectors 3: Pickles ------------------------------- -8: [17:55:16] Test RealValue Vectors 4: Vector Operations ------------------------------- -11: Randomness seeded to: 3469237816 +8: [14:17:36] Done +8: [14:17:36] Test DiscreteValue Vectors 1 ---------------------------- +8: [14:17:36] Expected failure: Value out of range +8: [14:17:36] Expected failure: Value out of range +8: [14:17:36] Expected failure: Value out of range +8: [14:17:36] Expected failure: Value out of range +8: [14:17:36] Expected failure: Value out of range +8: [14:17:36] Test DiscreteValue Vectors 2 ------------------------------ +8: [14:17:36] Test DiscreteValue Vectors 3 --------------------------- +8: [14:17:36] Test DiscreteValue Operations ----------------------------- +8: [14:17:36] Test DiscreteValue Operations 2 -------------------------- +8: [14:17:36] Test SparseIntVect ------------------------------------ +8: [14:17:36] Test SparseIntVect Serialization -------------------------- +8: [14:17:36] Test BitVect Serialization ------------------------------- +8: [14:17:36] Test BitVect to FPS ------------------------------- +8: [14:17:36] Test BitVect to binary string ------------------------------- +8: [14:17:36] Test Similarity Measures BitVect ------------------------------- +8: [14:17:36] Test Similarity Measures SparseBitVect ------------------------------- +8: [14:17:36] Test BitVect with all ones ------------------------------- +8: [14:17:36] Test Explicit BitVects: Concatenation Operation ------------------------------- +8: [14:17:36] Test bitmap operations ------------------------------- +8: [14:17:36] Test bitmaps as properties ------------------------------- +8: [14:17:36] Test #3944: SparseIntVect copy constructor and assignment operators not clearing existing data------------------------------- +8: [14:17:36] Test RealValue Vectors 1: Constructors and Accessing Values ------------------------------- +8: [14:17:36] Test RealValue Vectors 2: L1Norm ------------------------------- +8: [14:17:36] Test RealValue Vectors 3: Pickles ------------------------------- +8: [14:17:36] Test RealValue Vectors 4: Vector Operations ------------------------------- +11: Randomness seeded to: 20401551 11: =============================================================================== 11: All tests passed (3 assertions in 1 test case) 11: @@ -15834,8 +16218,8 @@ 17: testPointOps2D 17: **************************************** 17: test12D -17: ref1: 2.9925 3.58475 ref2: 3.70957 0.400842 -17: pt1: 1.14683 4.81395 pt2: 1.57525 1.8571 +17: ref1: 1.048 3.13786 ref2: 3.15594 0.584057 +17: pt1: 0.238058 4.46631 pt2: 4.16898 2.88358 17: **************************************** 17: test23D 17: **************************************** @@ -15881,21 +16265,21 @@ 19: --------------------------------- 19: test4UniformRealValueGrid3DOps 19: -20: Randomness seeded to: 3174357906 +20: Randomness seeded to: 1932592786 20: =============================================================================== 20: All tests passed (50 assertions in 5 test cases) 20: -22: [17:55:16] ----------------------------------------- -22: [17:55:16] Testing RDNumerics: vectors and matrices Code -22: [17:55:16] --------------------------------------- -22: [17:55:16] test1Vector -22: [17:55:16] --------------------------------------- -22: [17:55:16] test2Matrix -22: [17:55:16] --------------------------------------- -22: [17:55:16] test3SquareMatrix -22: [17:55:16] --------------------------------------- -22: [17:55:16] test4SymmMatrix -23: Randomness seeded to: 230869060 +22: [14:17:36] ----------------------------------------- +22: [14:17:36] Testing RDNumerics: vectors and matrices Code +22: [14:17:36] --------------------------------------- +22: [14:17:36] test1Vector +22: [14:17:36] --------------------------------------- +22: [14:17:36] test2Matrix +22: [14:17:36] --------------------------------------- +22: [14:17:36] test3SquareMatrix +22: [14:17:36] --------------------------------------- +22: [14:17:36] test4SymmMatrix +23: Randomness seeded to: 367624507 23: =============================================================================== 23: All tests passed (76 assertions in 3 test cases) 23: @@ -15916,7 +16300,7 @@ 26: ------------------------------------- 26: Testing BFGS optimization. 26: done -27: Randomness seeded to: 2083073431 +27: Randomness seeded to: 3258073861 27: =============================================================================== 27: All tests passed (20 assertions in 2 test cases) 27: @@ -15972,23 +16356,49 @@ 28: done 28: ------------------------------------- 28: Unit test for UFF butane scan. - 1/236 Test #3: testDict ............................... Passed 0.11 sec - 2/236 Test #4: testRDValue ............................ Passed 0.11 sec - 3/236 Test #6: dictTestsCatch ......................... Passed 0.10 sec - 4/236 Test #7: logTestsCatch .......................... Passed 0.10 sec - 5/236 Test #8: testDataStructs ........................ Passed 0.10 sec - 6/236 Test #9: testFPB ................................ Passed 0.10 sec - 7/236 Test #10: testMultiFPB ........................... Passed 0.10 sec - 8/236 Test #11: catchDataStructs ....................... Passed 0.10 sec - 9/236 Test #17: testTransforms ......................... Passed 0.09 sec - 10/236 Test #18: testGrid ............................... Passed 0.09 sec - 11/236 Test #19: testRealValueGrid ...................... Passed 0.09 sec - 12/236 Test #20: geometryTestsCatch ..................... Passed 0.09 sec - 13/236 Test #22: testMatrices ........................... Passed 0.08 sec - 14/236 Test #23: testConrec ............................. Passed 0.08 sec - 15/236 Test #24: testAlignment .......................... Passed 0.08 sec - 16/236 Test #26: testOptimizer .......................... Passed 0.08 sec - 17/236 Test #27: ForceFieldsCatch ....................... Passed 0.08 sec +29: ------------------------------------- +29: Official MMFF validation suite. +31: *********************************************************** +31: test1 +31: *********************************************************** +31: testIssue216 +31: Rows: 4 Columns: 4 +31: 0 1 1 1 +31: 1 0 1 1 +31: 1 1 0 1 +31: 1 1 1 0 +31: *********************************************************** +31: + 1/236 Test #3: testDict ............................... Passed 0.71 sec + 2/236 Test #4: testRDValue ............................ Passed 0.69 sec + 3/236 Test #6: dictTestsCatch ......................... Passed 0.66 sec + 4/236 Test #7: logTestsCatch .......................... Passed 0.65 sec + 5/236 Test #8: testDataStructs ........................ Passed 0.64 sec + 6/236 Test #9: testFPB ................................ Passed 0.63 sec + 7/236 Test #10: testMultiFPB ........................... Passed 0.61 sec + 8/236 Test #11: catchDataStructs ....................... Passed 0.59 sec + 9/236 Test #17: testTransforms ......................... Passed 0.46 sec + 10/236 Test #18: testGrid ............................... Passed 0.44 sec + 11/236 Test #19: testRealValueGrid ...................... Passed 0.42 sec + 12/236 Test #20: geometryTestsCatch ..................... Passed 0.41 sec + 13/236 Test #22: testMatrices ........................... Passed 0.39 sec + 14/236 Test #23: testConrec ............................. Passed 0.37 sec + 15/236 Test #24: testAlignment .......................... Passed 0.35 sec + 16/236 Test #26: testOptimizer .......................... Passed 0.33 sec + 17/236 Test #27: ForceFieldsCatch ....................... Passed 0.31 sec + 18/236 Test #31: testDistGeom ........................... Passed 0.23 sec +test 41 + Start 41: graphmolMemTest1 + +41: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolMemTest1 +41: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol +41: Test timeout computed to be: 1500 +test 42 + Start 42: resMolSupplierTest + +42: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/resMolSupplierTest +42: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol +42: Test timeout computed to be: 1500 test 43 Start 43: molBundleTest @@ -16085,44 +16495,34 @@ 58: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTest1 58: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse 58: Test timeout computed to be: 1500 -test 59 - Start 59: smiTest2 - -59: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTest2 -59: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse -59: Test timeout computed to be: 1500 -31: *********************************************************** -31: test1 -31: *********************************************************** -31: testIssue216 -31: Rows: 4 Columns: 4 -31: 0 1 1 1 -31: 1 0 1 1 -31: 1 1 0 1 -31: 1 1 1 0 -31: *********************************************************** -31: - 18/236 Test #31: testDistGeom ........................... Passed 2.41 sec -29: ------------------------------------- -29: Official MMFF validation suite. -29: -29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_dative.sdf... + 19/236 Test #1: testCoordGen ........................... Passed 1.04 sec 33: 33: 33: 33: COPY - 19/236 Test #33: graphmolcpTest ......................... Passed 2.41 sec -34: [17:55:16] ---------------------- Test1 -34: [17:55:16] Done! -34: [17:55:16] ---------------------- Test2 -34: [17:55:16] Done! -34: [17:55:16] ---------------------- Test3 -34: [17:55:16] Done! -34: [17:55:16] ---------------------- Test4 -34: [17:55:16] Done! -34: [17:55:16] ---------------------- Test5 -34: [17:55:16] Done! -34: [17:55:16] + 20/236 Test #33: graphmolcpTest ......................... Passed 0.50 sec +14: ...... +14: ---------------------------------------------------------------------- +14: Ran 6 tests in 0.015s +14: +14: OK + 21/236 Test #14: pyRealValueVect ........................ Passed 0.84 sec +13: ...... +13: ---------------------------------------------------------------------- +13: Ran 6 tests in 0.023s +13: +13: OK +34: [14:17:36] ---------------------- Test1 +34: [14:17:37] Done! +34: [14:17:37] ---------------------- Test2 +34: [14:17:37] Done! +34: [14:17:37] ---------------------- Test3 +34: [14:17:37] Done! +34: [14:17:37] ---------------------- Test4 +34: [14:17:37] Done! +34: [14:17:37] ---------------------- Test5 +34: [14:17:37] Done! +34: [14:17:37] 34: 34: **** 34: Pre-condition Violation @@ -16134,52 +16534,52 @@ 34: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 34: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 34: 2# RDKit::QueryAtom::expandQuery(Queries::Query*, Queries::CompositeQueryType, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -34: 3# 0x000056069D18E7EB in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolqueryTest -34: 4# 0x000056069D18C0AB in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolqueryTest -34: 5# 0x00007F3B5D033CA8 in /lib/x86_64-linux-gnu/libc.so.6 +34: 3# 0x00005616CE8317EB in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolqueryTest +34: 4# 0x00005616CE82F0AB in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolqueryTest +34: 5# 0x00007F5166E33CA8 in /lib/x86_64-linux-gnu/libc.so.6 34: 6# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -34: 7# 0x000056069D18C121 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolqueryTest +34: 7# 0x00005616CE82F121 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolqueryTest 34: ---------- 34: **** 34: -34: [17:55:16] Done! -34: [17:55:16] ---------------------- Test issue 2892580 -34: [17:55:16] Done! -34: [17:55:16] ---------------------- Test github issue 53: query molecules not matching [R] -34: [17:55:16] Done! -34: [17:55:16] ---------------------- Test queries using qualifiers instead of == -34: [17:55:16] Done! -34: [17:55:16] ---------------------- Test Github issue 165: radicals not used in atom-atom matching -34: [17:55:16] Done! -34: [17:55:16] ---------------------- Test extra atom queries -34: [17:55:16] Done! -34: [17:55:16] ---------------------- Test extra bond queries -34: [17:55:16] Done! -34: [17:55:16] ---------------------- Test num heteroatom neighbor queries -34: [17:55:16] Done! -34: [17:55:16] ---------------------- Test atom type queries -34: [17:55:16] Done! -34: [17:55:16] ---------------------- Test Github #2471: dummy atom queries are flagged as complex -34: [17:55:16] Done! -34: [17:55:16] ---------------------- Testing hasBondTypeQuery() and hasComplexBondTypeQuery() -34: [17:55:16] Done! - 20/236 Test #34: graphmolqueryTest ...................... Passed 2.41 sec +34: [14:17:37] Done! +34: [14:17:37] ---------------------- Test issue 2892580 +34: [14:17:37] Done! +34: [14:17:37] ---------------------- Test github issue 53: query molecules not matching [R] +34: [14:17:37] Done! +34: [14:17:37] ---------------------- Test queries using qualifiers instead of == +34: [14:17:37] Done! +34: [14:17:37] ---------------------- Test Github issue 165: radicals not used in atom-atom matching +34: [14:17:37] Done! +34: [14:17:37] ---------------------- Test extra atom queries +34: [14:17:37] Done! +34: [14:17:37] ---------------------- Test extra bond queries +34: [14:17:37] Done! +34: [14:17:37] ---------------------- Test num heteroatom neighbor queries +34: [14:17:37] Done! +34: [14:17:37] ---------------------- Test atom type queries +34: [14:17:37] Done! +34: [14:17:37] ---------------------- Test Github #2471: dummy atom queries are flagged as complex +34: [14:17:37] Done! +34: [14:17:37] ---------------------- Testing hasBondTypeQuery() and hasComplexBondTypeQuery() +34: [14:17:37] Done! + 22/236 Test #34: graphmolqueryTest ...................... Passed 0.49 sec 35: 1 1 2 35: 1 1 1 35: 2 1 0.75 35: path: 2 -35: [17:55:16] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored -35: [17:55:16] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored -35: [17:55:16] Explicit valence for atom # 0 B, 5, is greater than permitted -35: [17:55:16] Explicit valence for atom # 1 C, 5, is greater than permitted -35: [17:55:16] Explicit valence for atom # 1 C, 5, is greater than permitted -35: [17:55:16] Explicit valence for atom # 1 C, 5, is greater than permitted -35: [17:55:16] Explicit valence for atom # 1 Si, 7, is greater than permitted +35: [14:17:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored +35: [14:17:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored +35: [14:17:37] Explicit valence for atom # 0 B, 5, is greater than permitted +35: [14:17:37] Explicit valence for atom # 1 C, 5, is greater than permitted +35: [14:17:37] Explicit valence for atom # 1 C, 5, is greater than permitted +35: [14:17:37] Explicit valence for atom # 1 C, 5, is greater than permitted +35: [14:17:37] Explicit valence for atom # 1 Si, 7, is greater than permitted 35: smi: Cc1ccc(S(=O)(=O)/N=C2\CC(=N\C(C)(C)C)/C2=N\C(C)(C)C)cc1 -35: [17:55:17] non-ring atom 0 marked aromatic -35: [17:55:17] non-ring atom 0 marked aromatic -35: [17:55:17] Conflicting single bond directions around double bond at index 17. -35: [17:55:17] BondStereo set to STEREONONE and single bond directions set to NONE. +35: [14:17:37] non-ring atom 0 marked aromatic +35: [14:17:37] non-ring atom 0 marked aromatic +35: [14:17:37] Conflicting single bond directions around double bond at index 17. +35: [14:17:37] BondStereo set to STEREONONE and single bond directions set to NONE. 35: starting ring finding 35: done 35: starting ring finding @@ -16196,27 +16596,28 @@ 35: starting ring finding 35: done 35: smiles: CC[C@]1(C(=O)c([nH])n)CC[C@](C)(O)CC1 -35: [17:55:17] WARNING: not removing hydrogen atom with dummy atom neighbors -35: ------------------------------- -35: [17:55:17] Explicit valence for atom # 0 N, 4, is greater than permitted -35: [17:55:17] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -35: [17:55:17] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -35: [17:55:17] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -35: [17:55:17] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -35: [17:55:17] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -35: [17:55:17] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -35: [17:55:17] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -35: [17:55:17] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -35: -35: [17:55:17] WARNING: not removing hydrogen atom with dummy atom neighbors -37: [17:55:16] ------------------------------------- -37: [17:55:16] Testing String Pickle Roundtrips. -37: [17:55:17] done -37: [17:55:17] ------------------------------------- -37: [17:55:17] Testing reading existing pickle file (v2). -37: [17:55:17] done -37: [17:55:17] ------------------------------------- -37: [17:55:17] Testing combining molecules using pickles. +36: -------------------------- +36: -------------------------- +36: C/C=C/C(C)Cl +36: [14:17:37] Conflicting single bond directions around double bond at index 2. +36: [14:17:37] BondStereo set to STEREONONE and single bond directions set to NONE. +36: [14:17:37] Conflicting single bond directions around double bond at index 4. +36: [14:17:37] BondStereo set to STEREONONE and single bond directions set to NONE. +36: [14:17:37] Conflicting single bond directions around double bond at index 15. +36: [14:17:37] BondStereo set to STEREONONE and single bond directions set to NONE. +36: [14:17:37] Conflicting single bond directions around double bond at index 2. +36: [14:17:37] BondStereo set to STEREONONE and single bond directions set to NONE. +36: [14:17:37] Conflicting single bond directions around double bond at index 1. +36: [14:17:37] BondStereo set to STEREONONE and single bond directions set to NONE. +36: -------------------------------------------------- +37: [14:17:37] ------------------------------------- +37: [14:17:37] Testing String Pickle Roundtrips. +37: [14:17:37] done +37: [14:17:37] ------------------------------------- +37: [14:17:37] Testing reading existing pickle file (v2). +37: [14:17:37] done +37: [14:17:37] ------------------------------------- +37: [14:17:37] Testing combining molecules using pickles. 37: Atoms: 37: 0 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: SP3 37: 1 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: SP3 @@ -16233,37 +16634,37 @@ 37: 4 4->5 order: 1 37: 5 5->6 order: 1 37: 6 6->3 order: 1 -37: [17:55:17] done -37: [17:55:17] ------------------------------------- -37: [17:55:17] Testing Issue164: Roundtrip Pickle Failure. -37: [17:55:17] done -37: [17:55:17] ------------------------------------- -37: [17:55:17] Testing Issue219: Pickle Failure with Conformations. -37: [17:55:17] done -37: [17:55:17] ------------------------------------- -37: [17:55:17] Testing Issue220: Pickle problems with bond stereochemistry. -37: [17:55:17] done -37: [17:55:17] ------------------------------------- -37: [17:55:17] Testing query serialization. -37: [17:55:17] C=[$(C=O)] -37: [17:55:17] S(=O)(=O)-[C&H2][F,Br,I,Cl] S(=O)(=O)-[C&H2][F,Br,I,Cl] -37: [17:55:17] done -37: [17:55:17] ------------------------------------- -37: [17:55:17] Testing radical handling in pickles. -37: [17:55:17] done -37: [17:55:17] done -37: [17:55:17] ------------------------------------- -37: [17:55:17] Testing sf.net issue 2788233. -37: [17:55:17] done -37: [17:55:17] ------------------------------------- -37: [17:55:17] Testing sf.net issue 3202580. +37: [14:17:37] done +37: [14:17:37] ------------------------------------- +37: [14:17:37] Testing Issue164: Roundtrip Pickle Failure. +37: [14:17:37] done +37: [14:17:37] ------------------------------------- +37: [14:17:37] Testing Issue219: Pickle Failure with Conformations. +37: [14:17:37] done +37: [14:17:37] ------------------------------------- +37: [14:17:37] Testing Issue220: Pickle problems with bond stereochemistry. +37: [14:17:37] done +37: [14:17:37] ------------------------------------- +37: [14:17:37] Testing query serialization. +37: [14:17:37] C=[$(C=O)] +37: [14:17:37] S(=O)(=O)-[C&H2][F,Br,I,Cl] S(=O)(=O)-[C&H2][F,Br,I,Cl] +37: [14:17:37] done +37: [14:17:37] ------------------------------------- +37: [14:17:37] Testing radical handling in pickles. +37: [14:17:37] done +37: [14:17:37] done +37: [14:17:37] ------------------------------------- +37: [14:17:37] Testing sf.net issue 2788233. +37: [14:17:37] done +37: [14:17:37] ------------------------------------- +37: [14:17:37] Testing sf.net issue 3202580. 37: mass! 13.0034 -37: [17:55:17] done -37: [17:55:17] ------------------------------------- -37: [17:55:17] Testing sf.net issue 3316407. -37: [17:55:17] done -37: [17:55:17] ------------------------------------- -37: [17:55:17] Testing sf.net issue 3496759. +37: [14:17:37] done +37: [14:17:37] ------------------------------------- +37: [14:17:37] Testing sf.net issue 3316407. +37: [14:17:37] done +37: [14:17:37] ------------------------------------- +37: [14:17:37] Testing sf.net issue 3496759. 37: smi match: *C *C 37: smi match: **=* **=* 37: smi match: [N-]=[N+]=NC=O [N-]=[N+]=NC=O @@ -16385,6 +16786,47 @@ 37: smi match: NC(S)=N[SH](=O)=O NC(S)=N[SH](=O)=O 37: smi match: N=C(N)S N=C(N)S 37: smi match: NC(=O)Oc1ccccc1 NC(=O)Oc1ccccc1 +38: [14:17:37] done + 23/236 Test #38: graphmoltestPicklerGlobalSetting ....... Passed 0.43 sec + 24/236 Test #39: graphmolIterTest ....................... Passed 0.42 sec +40: [14:17:37] Testing the hanoi sort +40: [14:17:37] populating vectors +test 59 + Start 59: smiTest2 + +59: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTest2 +59: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse +59: Test timeout computed to be: 1500 +test 60 + Start 60: cxsmilesTest + +60: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/cxsmilesTest +60: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse +60: Test timeout computed to be: 1500 +test 61 + Start 61: smaTest1 + +61: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smaTest1 +61: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse +61: Test timeout computed to be: 1500 +test 62 + Start 62: smiTestCatch + +62: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse +62: Test timeout computed to be: 1500 +test 63 + Start 63: nontetrahedralCatch + +63: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/nontetrahedralCatch +63: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse +63: Test timeout computed to be: 1500 +test 64 + Start 64: v2smiTestCatch + +64: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/v2smiTestCatch +64: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse +64: Test timeout computed to be: 1500 37: smi match: NC=S NC=S 37: smi match: NC(N)=S NC(N)=S 37: smi match: C=CN C=CN @@ -16616,575 +17058,68 @@ 37: smi match: N~N~N N~N~N 37: smi match: *N=N* *N=N* 37: smi match: *CC[OH] *CC[OH] -37: smi match: *CC[OH] *CC[OH] -37: smi match: *=CCC(=O)[OH] *=CCC(=O)[OH] -37: smi match: O=C([OH])CC[OH] O=C([OH])CC[OH] -37: smi match: *CCC(=O)[OH] *CCC(=O)[OH] -37: smi match: CC(=O)CC(=O)[OH] CC(=O)CC(=O)[OH] -37: smi match: *OC(=O)CC(C)=O *OC(=O)CC(C)=O -37: smi match: *OC(*)=O *OC(*)=O -37: smi match: *C(=O)[OH] *C(=O)[OH] -37: smi match: O=C[OH] O=C[OH] -37: smi match: *OC(=O)O* *OC(=O)O* -37: smi match: * * -37: smi match: *OC(=O)Cl *OC(=O)Cl -37: smi match: *C#N *C#N -37: smi match: NCC(=O)NCC=O NCC(=O)NCC=O -37: smi match: SS SS -37: smi match: * * -37: smi match: *=* *=* -37: smi match: *=* *=* -37: smi match: *=* *=* -37: smi match: *=* *=* -37: smi match: C1CO1 C1CO1 -37: smi match: *OC(*)=O *OC(*)=O -37: smi match: * * -37: smi match: *O*[OH] *O*[OH] -37: smi match: COC(C)(C)O COC(C)(C)O -37: smi match: *[OH] *[OH] -37: smi match: ** ** -37: smi match: C=N[NH2] C=N[NH2] -37: smi match: C=NC=O C=NC=O -37: smi match: * * -37: smi match: C#NC C#NC -37: smi match: CN=C=O CN=C=O -37: smi match: CN=C=S CN=C=S -37: smi match: *OC(*)(*)O* *OC(*)(*)O* -37: smi match: *C(*)=O *C(*)=O -37: smi match: C~C~C~C~C~C~C C~C~C~C~C~C~C -37: smi match: *~*=O *~*=O -37: smi match: *~*=O *~*=O -37: smi match: OC(=O)CC(=O)[OH] OC(=O)CC(=O)[OH] -37: smi match: * * -37: smi match: *C#N *C#N -37: smi match: *N(=O)~O *N(=O)~O -37: smi match: N N -37: smi match: OC(=O)C(O)=O OC(=O)C(O)=O -37: smi match: C=NO C=NO -37: smi match: O~O O~O -37: smi match: c[OH] c[OH] -37: smi match: O=P(~[OH])~O O=P(~[OH])~O -37: smi match: CO~P(=O)~O CO~P(=O)~O -37: smi match: O=P(~[OH])(~O)~O O=P(~[OH])(~O)~O -37: smi match: CO~P(=O)(~O)~O CO~P(=O)(~O)~O -37: smi match: O=P(~O)~O O=P(~O)~O -37: smi match: O=P(~O)(~O)~O O=P(~O)(~O)~O -37: smi match: C[NH2] C[NH2] -37: smi match: O~*1~**~*(~O)~**~1 O~*1~**~*(~O)~**~1 -37: smi match: * * -37: smi match: *1~*~*~C2~C(~*~1)~*~*~C1~C3~*~*~*~C~3~*~*~C~2~1 *1~*~*~C2~C(~*~1)~*~*~C1~C3~*~*~*~C~3~*~*~C~2~1 -37: smi match: CS(C)~O CS(C)~O -37: smi match: CS(C)(~O)~O CS(C)(~O)~O -37: smi match: CS(N)(~O)~O CS(N)(~O)~O -37: smi match: CS([OH])(~O)~O CS([OH])(~O)~O -37: smi match: COS(C)(~O)~O COS(C)(~O)~O -37: smi match: *S(C)(~O)~O *S(C)(~O)~O -37: smi match: CN(C)C CN(C)C -37: smi match: *c1nnc(=N)s1 *c1nnc(=N)s1 -37: smi match: *C(*)=S *C(*)=S -37: smi match: *OC(*)=S *OC(*)=S -37: smi match: * * -37: smi match: C[SH] C[SH] -37: smi match: c[SH] c[SH] -37: smi match: NC(N)=S NC(N)=S -37: smi match: * * -37: smi match: ***** ***** -37: smi match: NC(N)=O NC(N)=O -37: [17:55:17] done -37: [17:55:17] ------------------------------------- -37: [17:55:17] Testing sf.net issue 280. -37: [17:55:17] done -37: [17:55:17] ------------------------------------- -37: [17:55:17] Testing sf.net issue 285. -37: [17:55:17] done -37: [17:55:17] done -37: [17:55:17] done -37: [17:55:17] done -37: [17:55:17] done -37: [17:55:17] done -37: [17:55:17] done -37: [17:55:17] ------------------------------------- -37: [17:55:17] Testing Github2441: Add RDProps interface to Conformers. -37: [17:55:17] done -37: [17:55:17] ------------------------------------- -37: [17:55:17] Testing Issue2510: Pickle Confs as double. -37: [17:55:17] done -37: [17:55:17] ------------------------------------- -37: [17:55:17] Testing Github #2465: Negative atom-map numbers cause depickling to fail. -37: [17:55:17] done -37: [17:55:17] ------------------------------------- -37: [17:55:17] Testing loading pickled mols with conformers -37: [17:55:17] done -37: [17:55:17] ------------------------------------- -37: [17:55:17] Testing conformer reading/writing options -37: [17:55:17] done -37: [17:55:17] ------------------------------------- -37: [17:55:17] Testing property reading options -37: [17:55:17] done -37: [17:55:17] ------------------------------------- -37: [17:55:17] Testing property reading options -37: [17:55:17] done -37: [17:55:17] ------------------------------------- -37: [17:55:17] Testing boost::serialization integration -37: [17:55:17] done -37: [17:55:17] ------------------------------------- -37: [17:55:17] Testing github issue 6036 -38: [17:55:16] done - 21/236 Test #38: graphmoltestPicklerGlobalSetting ....... Passed 2.41 sec - 22/236 Test #39: graphmolIterTest ....................... Passed 2.41 sec -40: [17:55:16] Testing the hanoi sort -40: [17:55:16] populating vectors - 23/236 Test #41: graphmolMemTest1 ....................... Passed 2.40 sec -test 60 - Start 60: cxsmilesTest - -60: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/cxsmilesTest -60: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse -60: Test timeout computed to be: 1500 -test 61 - Start 61: smaTest1 - -61: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smaTest1 -61: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse -61: Test timeout computed to be: 1500 -test 62 - Start 62: smiTestCatch - -62: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse -62: Test timeout computed to be: 1500 -test 63 - Start 63: nontetrahedralCatch - -63: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/nontetrahedralCatch -63: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse -63: Test timeout computed to be: 1500 -test 64 - Start 64: v2smiTestCatch - -64: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/v2smiTestCatch -64: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse -64: Test timeout computed to be: 1500 -test 65 - Start 65: testDepictor - -65: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/testDepictor -65: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor -65: Test timeout computed to be: 1500 -28: done -36: -------------------------- -36: -------------------------- -36: C/C=C/C(C)Cl -36: [17:55:17] Conflicting single bond directions around double bond at index 2. -36: [17:55:17] BondStereo set to STEREONONE and single bond directions set to NONE. -36: [17:55:17] Conflicting single bond directions around double bond at index 4. -36: [17:55:17] BondStereo set to STEREONONE and single bond directions set to NONE. -36: [17:55:17] Conflicting single bond directions around double bond at index 15. -36: [17:55:17] BondStereo set to STEREONONE and single bond directions set to NONE. -36: [17:55:17] Conflicting single bond directions around double bond at index 2. -36: [17:55:17] BondStereo set to STEREONONE and single bond directions set to NONE. -36: [17:55:17] Conflicting single bond directions around double bond at index 1. -36: [17:55:17] BondStereo set to STEREONONE and single bond directions set to NONE. -36: -------------------------------------------------- -1: cyclosporine a -1: RDKit 2D -1: -1: 85 85 0 0 0 0 0 0 0 0999 V2000 -1: 1.4840 -0.8529 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 0.6174 -1.3521 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 0.6176 -2.3509 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 1.4860 -2.8479 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 1.4912 -3.8491 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1: 2.3504 -2.3385 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1: 2.3352 -1.3311 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 3.1902 -0.7993 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 3.1580 0.1961 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1: 4.0642 -1.2607 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1: 4.9260 -0.7295 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 4.9144 0.3303 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 5.7766 0.8337 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1: 4.0008 0.8409 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1: 3.8596 1.9125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 2.8162 2.2071 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 2.2038 1.4219 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1: 2.2560 3.1855 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1: 2.5280 4.2325 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 1.7128 4.8927 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 1.8530 5.8895 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1: 0.7676 4.5077 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1: -0.0820 5.0835 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -0.9744 4.6151 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -1.8344 5.1337 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1: -0.9792 3.6203 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1: -1.8192 3.0813 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -2.7974 3.5817 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -2.7998 4.5809 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1: -3.7790 3.0789 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1: -3.8812 2.0705 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -3.1202 1.6015 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -2.4194 2.0931 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1: -3.0590 0.6211 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1: -3.8626 0.0983 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -3.8096 -0.8961 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -4.6470 -1.4375 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1: -2.9122 -1.3587 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1: -2.8776 -2.3565 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -1.9982 -2.8425 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -1.1382 -2.3311 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1: -1.9886 -3.8459 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1: -1.1202 -4.3461 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -0.2526 -3.8491 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 0.6116 -4.3521 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1: -0.2494 -2.8505 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1: -1.1228 -5.3475 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -0.2584 -5.8507 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 0.6092 -5.3541 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -0.2624 -6.8511 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 0.6018 -7.3547 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 0.5982 -8.3547 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 1.4624 -8.8579 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -1.9906 -5.8449 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1: -2.8520 -4.3501 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -3.7288 -2.8719 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -3.7098 -3.8701 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -4.6032 -2.3871 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -2.0646 -0.8235 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -4.7362 0.5679 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -5.5794 0.0605 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -5.5618 -0.9361 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -6.4498 0.5487 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -2.1628 0.1727 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -4.7698 1.6253 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -5.5952 2.1745 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -6.4896 1.7311 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -5.5292 3.1711 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -4.6054 3.6407 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -1.7186 2.0867 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -0.0328 6.0847 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 3.4396 4.6417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 3.4580 5.6909 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 4.3220 6.1985 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 2.5836 6.2065 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 1.2682 3.0557 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 4.6630 2.5215 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 5.5876 2.1073 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 4.5648 3.5065 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 5.7968 -1.2481 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 6.6786 -0.7913 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 7.5218 -1.3355 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 6.7252 0.2017 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 4.0970 -2.2659 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 3.2220 -2.8307 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 1 2 1 0 -1: 3 2 1 1 -1: 3 4 1 0 -1: 4 5 2 0 -1: 4 6 1 0 -1: 6 7 1 0 -1: 7 8 1 0 -1: 8 9 2 0 -1: 8 10 1 0 -1: 10 11 1 0 -1: 11 12 1 0 -1: 12 13 2 0 -1: 12 14 1 0 -1: 14 15 1 0 -1: 15 16 1 0 -1: 16 17 2 0 -1: 16 18 1 0 -1: 18 19 1 0 -1: 19 20 1 0 -1: 20 21 2 0 -1: 20 22 1 0 -1: 22 23 1 0 -1: 23 24 1 0 -1: 24 25 2 0 -1: 24 26 1 0 -1: 26 27 1 0 -1: 27 28 1 0 -1: 28 29 2 0 -1: 28 30 1 0 -1: 30 31 1 0 -1: 31 32 1 0 -1: 32 33 2 0 -1: 32 34 1 0 -1: 34 35 1 0 -1: 35 36 1 0 -1: 36 37 2 0 -1: 36 38 1 0 -1: 38 39 1 0 -1: 39 40 1 0 -1: 40 41 2 0 -1: 40 42 1 0 -1: 43 42 1 6 -1: 43 44 1 0 -1: 44 45 2 0 -1: 44 46 1 0 -1: 43 47 1 0 -1: 47 48 1 0 -1: 48 49 1 6 -1: 48 50 1 0 -1: 50 51 1 0 -1: 51 52 2 0 -1: 52 53 1 0 -1: 47 54 1 1 -1: 42 55 1 0 -1: 39 56 1 6 -1: 56 57 1 0 -1: 56 58 1 0 -1: 38 59 1 0 -1: 35 60 1 6 -1: 60 61 1 0 -1: 61 62 1 0 -1: 61 63 1 0 -1: 34 64 1 0 -1: 31 65 1 6 -1: 65 66 1 0 -1: 66 67 1 0 -1: 66 68 1 0 -1: 30 69 1 0 -1: 27 70 1 6 -1: 23 71 1 6 -1: 19 72 1 6 -1: 72 73 1 0 -1: 73 74 1 0 -1: 73 75 1 0 -1: 18 76 1 0 -1: 15 77 1 6 -1: 77 78 1 0 -1: 77 79 1 0 -1: 11 80 1 6 -1: 80 81 1 0 -1: 81 82 1 0 -1: 81 83 1 0 -1: 10 84 1 0 -1: 6 85 1 0 -1: 46 3 1 0 -1: M END -1: -1: single-double -1: RDKit 2D -1: -1: 17 16 0 0 0 0 0 0 0 0999 V2000 -1: -6.9282 -0.2298 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -6.0618 0.2696 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -5.1962 -0.2312 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -4.3298 0.2682 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1: -3.4642 -0.2326 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -2.5978 0.2668 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -1.7322 -0.2340 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1: -0.8658 0.2654 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -0.0002 -0.2352 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1: 0.8662 0.2640 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 1.7318 -0.2366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 2.5982 0.2626 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 3.4638 -0.2380 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 4.3302 0.2612 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 5.1958 -0.2394 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 6.0622 0.2598 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1: 6.9278 -0.2408 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 1 2 1 0 -1: 2 3 1 0 -1: 3 4 1 0 -1: 4 5 1 0 -1: 5 6 2 3 -1: 6 7 1 0 -1: 7 8 1 0 -1: 8 9 1 0 -1: 9 10 1 0 -1: 10 11 2 3 -1: 11 12 1 0 -1: 12 13 2 3 -1: 13 14 1 0 -1: 14 15 2 3 -1: 15 16 1 0 -1: 16 17 1 0 -1: M END -1: -1: cis-trans -1: RDKit 2D -1: -1: 10 9 0 0 0 0 0 0 0 0999 V2000 -1: -3.6370 -0.2028 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1: -2.7706 -0.7022 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -1.9050 -0.2016 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -1.0386 -0.7008 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -0.1730 -0.2002 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 0.6934 -0.6994 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 1.5590 -0.1988 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 1.5582 0.8012 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 2.4238 1.3020 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 3.2902 0.8026 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1: 1 2 1 0 -1: 2 3 2 0 -1: 3 4 1 0 -1: 4 5 2 0 -1: 5 6 1 0 -1: 6 7 2 0 -1: 7 8 1 0 -1: 8 9 2 0 -1: 9 10 1 0 -1: M END -1: -1: admntn -1: RDKit 2D -1: -1: 10 12 0 0 0 0 0 0 0 0999 V2000 -1: 1.3505 -0.5360 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 0.5267 -1.1020 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -0.4629 -1.0366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -0.7523 0.0052 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -1.4741 0.5660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -0.4761 0.5032 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 0.3505 1.0730 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 1.0611 0.5080 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 0.0643 0.5686 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -0.1877 -0.5490 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 1 2 1 0 -1: 2 3 1 0 -1: 3 4 1 0 -1: 4 5 1 0 -1: 5 6 1 0 -1: 6 7 1 0 -1: 7 8 1 0 -1: 8 9 1 0 -1: 6 10 1 0 -1: 8 1 1 0 -1: 9 4 1 0 -1: 10 2 1 0 -1: M END -1: -1: github 4845 - nan coordinates but no crash -1: RDKit 2D -1: -1: 42 44 0 0 0 0 0 0 0 0999 V2000 -1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan O 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan O 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 -1: 1 2 1 0 -1: 2 3 1 0 -1: 2 4 2 0 -1: 4 5 1 0 -1: 5 6 3 0 -1: 6 7 1 0 -1: 7 8 2 0 -1: 8 9 1 0 -1: 9 10 3 0 -1: 10 11 1 0 -1: 11 12 2 0 -1: 12 13 1 0 -1: 13 14 3 0 -1: 14 15 1 0 -1: 15 16 2 0 -1: 16 17 1 0 -1: 16 18 1 0 -1: 12 19 1 0 -1: 19 20 2 0 -1: 20 21 1 0 -1: 20 22 1 0 -1: 19 23 1 0 -1: 23 24 3 0 -1: 24 25 1 0 -1: 25 26 1 0 -1: 26 27 2 0 -1: 27 28 2 0 -1: 26 29 1 0 -1: 29 30 3 0 -1: 8 31 1 0 -1: 31 32 2 0 -1: 32 33 1 0 -1: 32 34 1 0 -1: 31 35 1 0 -1: 35 36 3 0 -1: 36 37 1 0 -1: 37 38 2 0 -1: 37 39 1 0 -1: 39 40 2 0 -1: 40 41 1 0 -1: 40 42 1 0 -1: 39 4 1 0 -1: 15 7 1 0 -1: 30 11 1 0 -1: M END -1: +2: .... +2: ---------------------------------------------------------------------- +2: Ran 4 tests in 0.065s +2: +2: OK +16: ......... +16: ---------------------------------------------------------------------- +16: Ran 9 tests in 0.079s +16: +16: OK 15: ......... 15: ---------------------------------------------------------------------- -15: Ran 9 tests in 0.005s +15: Ran 9 tests in 0.023s 15: 15: OK -46: Randomness seeded to: 2488043647 -46: [17:55:19] WARNING: not removing hydrogen atom without neighbors -46: [17:55:19] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -46: [17:55:19] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -46: [17:55:19] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -46: [17:55:19] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -46: [17:55:19] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -46: [17:55:19] Explicit valence for atom # 1 N, 5, is greater than permitted -46: [17:55:19] Explicit valence for atom # 1 N, 6, is greater than permitted -46: [17:55:19] Explicit valence for atom # 1 N, 5, is greater than permitted -46: [17:55:19] Explicit valence for atom # 1 N, 5, is greater than permitted -46: [17:55:19] Explicit valence for atom # 2 O, 3, is greater than permitted -46: [17:55:19] Explicit valence for atom # 2 O, 3, is greater than permitted -46: [17:55:19] non-ring atom 2 marked aromatic -46: [17:55:19] non-ring atom 2 marked aromatic -46: [17:55:19] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -46: [17:55:19] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -46: [17:55:19] Can't kekulize mol. Unkekulized atoms: 1 2 3 -46: [17:55:19] Can't kekulize mol. Unkekulized atoms: 1 2 3 -46: [17:55:19] Can't kekulize mol. Unkekulized atoms: 0 1 2 -46: [17:55:19] Can't kekulize mol. Unkekulized atoms: 0 1 2 -46: [17:55:19] Explicit valence for atom # 1 O, 3, is greater than permitted -46: [17:55:19] Explicit valence for atom # 4 F, 2, is greater than permitted -46: [17:55:19] Can't kekulize mol. Unkekulized atoms: 6 7 8 -46: [17:55:19] Explicit valence for atom # 1 C, 5, is greater than permitted -46: [17:55:19] WARNING: not removing hydrogen atom with dummy atom neighbors -46: [17:55:19] WARNING: not removing hydrogen atom with dummy atom neighbors -46: [17:55:19] WARNING: not removing hydrogen atom with wedged bond -46: [17:55:19] WARNING: not removing hydrogen atom without neighbors -46: [17:55:19] WARNING: not removing hydrogen atom without neighbors -46: [17:55:19] WARNING: not removing hydrogen atom without neighbors -46: [17:55:19] WARNING: not removing hydrogen atom without neighbors -46: [17:55:19] Unreasonable formal charge on atom # 0. -46: [17:55:19] +32: ...... +32: ---------------------------------------------------------------------- +32: Ran 6 tests in 0.012s +32: +32: OK +25: ..... +25: ---------------------------------------------------------------------- +25: Ran 5 tests in 0.002s +25: +25: OK +25: Testing Alignment Wrapper code: +29: +29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_dative.sdf... +46: Randomness seeded to: 1099827180 +46: [14:17:37] WARNING: not removing hydrogen atom without neighbors +46: [14:17:37] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +46: [14:17:37] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +46: [14:17:37] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +46: [14:17:37] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +46: [14:17:37] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +46: [14:17:37] Explicit valence for atom # 1 N, 5, is greater than permitted +46: [14:17:37] Explicit valence for atom # 1 N, 6, is greater than permitted +46: [14:17:37] Explicit valence for atom # 1 N, 5, is greater than permitted +46: [14:17:37] Explicit valence for atom # 1 N, 5, is greater than permitted +46: [14:17:37] Explicit valence for atom # 2 O, 3, is greater than permitted +46: [14:17:37] Explicit valence for atom # 2 O, 3, is greater than permitted +46: [14:17:37] non-ring atom 2 marked aromatic +46: [14:17:37] non-ring atom 2 marked aromatic +46: [14:17:37] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +46: [14:17:37] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +46: [14:17:37] Can't kekulize mol. Unkekulized atoms: 1 2 3 +46: [14:17:37] Can't kekulize mol. Unkekulized atoms: 1 2 3 +46: [14:17:37] Can't kekulize mol. Unkekulized atoms: 0 1 2 +46: [14:17:37] Can't kekulize mol. Unkekulized atoms: 0 1 2 +46: [14:17:37] Explicit valence for atom # 1 O, 3, is greater than permitted +46: [14:17:37] Explicit valence for atom # 4 F, 2, is greater than permitted +46: [14:17:37] Can't kekulize mol. Unkekulized atoms: 6 7 8 +46: [14:17:37] Explicit valence for atom # 1 C, 5, is greater than permitted +46: [14:17:37] WARNING: not removing hydrogen atom with dummy atom neighbors +46: [14:17:37] WARNING: not removing hydrogen atom with dummy atom neighbors +46: [14:17:37] WARNING: not removing hydrogen atom with wedged bond +46: [14:17:37] WARNING: not removing hydrogen atom without neighbors +46: [14:17:37] WARNING: not removing hydrogen atom without neighbors +46: [14:17:37] WARNING: not removing hydrogen atom without neighbors +46: [14:17:37] WARNING: not removing hydrogen atom without neighbors +46: [14:17:37] Unreasonable formal charge on atom # 0. +46: [14:17:37] 46: 46: **** 46: Pre-condition Violation @@ -17196,20 +17131,20 @@ 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::ROMol::getAtomDegree(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x000055CFDABBA668 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x000055CFDAC07938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x000055CFDAC08458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x000055CFDAC088D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x000055CFDABD9F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x000055CFDABDA2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x000055CFDAB54DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007F2BE3633CA8 in /lib/x86_64-linux-gnu/libc.so.6 +46: 3# 0x000056415329A668 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x00005641532E7938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x00005641532E8458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x00005641532E88D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x00005641532B9F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x00005641532BA2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000564153234DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007F4AFF033CA8 in /lib/x86_64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -46: 12# 0x000055CFDAB54E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000564153234E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [17:55:19] +46: [14:17:37] 46: 46: **** 46: Pre-condition Violation @@ -17221,20 +17156,20 @@ 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::ROMol::getAtomDegree(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x000055CFDABBA6F2 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x000055CFDAC07938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x000055CFDAC08458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x000055CFDAC088D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x000055CFDABD9F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x000055CFDABDA2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x000055CFDAB54DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007F2BE3633CA8 in /lib/x86_64-linux-gnu/libc.so.6 +46: 3# 0x000056415329A6F2 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x00005641532E7938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x00005641532E8458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x00005641532E88D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x00005641532B9F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x00005641532BA2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000564153234DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007F4AFF033CA8 in /lib/x86_64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -46: 12# 0x000055CFDAB54E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000564153234E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [17:55:19] +46: [14:17:37] 46: 46: **** 46: Pre-condition Violation @@ -17246,20 +17181,20 @@ 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::ROMol::getAtomDegree(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x000055CFDABBA785 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x000055CFDAC07938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x000055CFDAC08458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x000055CFDAC088D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x000055CFDABD9F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x000055CFDABDA2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x000055CFDAB54DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007F2BE3633CA8 in /lib/x86_64-linux-gnu/libc.so.6 +46: 3# 0x000056415329A785 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x00005641532E7938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x00005641532E8458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x00005641532E88D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x00005641532B9F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x00005641532BA2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000564153234DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007F4AFF033CA8 in /lib/x86_64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -46: 12# 0x000055CFDAB54E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000564153234E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [17:55:19] +46: [14:17:37] 46: 46: **** 46: Pre-condition Violation @@ -17271,20 +17206,20 @@ 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::ROMol::getAtomNeighbors(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x000055CFDABBA870 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x000055CFDAC07938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x000055CFDAC08458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x000055CFDAC088D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x000055CFDABD9F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x000055CFDABDA2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x000055CFDAB54DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007F2BE3633CA8 in /lib/x86_64-linux-gnu/libc.so.6 +46: 3# 0x000056415329A870 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x00005641532E7938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x00005641532E8458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x00005641532E88D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x00005641532B9F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x00005641532BA2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000564153234DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007F4AFF033CA8 in /lib/x86_64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -46: 12# 0x000055CFDAB54E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000564153234E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [17:55:19] +46: [14:17:37] 46: 46: **** 46: Pre-condition Violation @@ -17296,20 +17231,20 @@ 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::ROMol::getAtomNeighbors(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x000055CFDABBA901 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x000055CFDAC07938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x000055CFDAC08458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x000055CFDAC088D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x000055CFDABD9F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x000055CFDABDA2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x000055CFDAB54DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007F2BE3633CA8 in /lib/x86_64-linux-gnu/libc.so.6 +46: 3# 0x000056415329A901 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x00005641532E7938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x00005641532E8458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x00005641532E88D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x00005641532B9F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x00005641532BA2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000564153234DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007F4AFF033CA8 in /lib/x86_64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -46: 12# 0x000055CFDAB54E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000564153234E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [17:55:19] +46: [14:17:37] 46: 46: **** 46: Pre-condition Violation @@ -17321,20 +17256,20 @@ 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::ROMol::getAtomNeighbors(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x000055CFDABBA99D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x000055CFDAC07938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x000055CFDAC08458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x000055CFDAC088D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x000055CFDABD9F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x000055CFDABDA2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x000055CFDAB54DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007F2BE3633CA8 in /lib/x86_64-linux-gnu/libc.so.6 +46: 3# 0x000056415329A99D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x00005641532E7938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x00005641532E8458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x00005641532E88D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x00005641532B9F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x00005641532BA2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000564153234DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007F4AFF033CA8 in /lib/x86_64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -46: 12# 0x000055CFDAB54E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000564153234E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [17:55:19] +46: [14:17:37] 46: 46: **** 46: Pre-condition Violation @@ -17346,20 +17281,20 @@ 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::ROMol::getAtomBonds(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x000055CFDABBB2B9 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x000055CFDAC07938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x000055CFDAC08458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x000055CFDAC088D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x000055CFDABD9F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x000055CFDABDA2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x000055CFDAB54DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007F2BE3633CA8 in /lib/x86_64-linux-gnu/libc.so.6 +46: 3# 0x000056415329B2B9 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x00005641532E7938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x00005641532E8458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x00005641532E88D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x00005641532B9F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x00005641532BA2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000564153234DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007F4AFF033CA8 in /lib/x86_64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -46: 12# 0x000055CFDAB54E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000564153234E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [17:55:19] +46: [14:17:37] 46: 46: **** 46: Pre-condition Violation @@ -17371,20 +17306,20 @@ 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::ROMol::getAtomBonds(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x000055CFDABBAB08 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x000055CFDAC07938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x000055CFDAC08458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x000055CFDAC088D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x000055CFDABD9F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x000055CFDABDA2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x000055CFDAB54DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007F2BE3633CA8 in /lib/x86_64-linux-gnu/libc.so.6 +46: 3# 0x000056415329AB08 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x00005641532E7938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x00005641532E8458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x00005641532E88D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x00005641532B9F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x00005641532BA2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000564153234DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007F4AFF033CA8 in /lib/x86_64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -46: 12# 0x000055CFDAB54E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000564153234E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [17:55:19] +46: [14:17:37] 46: 46: **** 46: Pre-condition Violation @@ -17396,20 +17331,20 @@ 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::ROMol::getAtomBonds(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x000055CFDABBABA2 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x000055CFDAC07938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x000055CFDAC08458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x000055CFDAC088D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x000055CFDABD9F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x000055CFDABDA2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x000055CFDAB54DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007F2BE3633CA8 in /lib/x86_64-linux-gnu/libc.so.6 +46: 3# 0x000056415329ABA2 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x00005641532E7938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x00005641532E8458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x00005641532E88D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x00005641532B9F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x00005641532BA2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000564153234DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007F4AFF033CA8 in /lib/x86_64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -46: 12# 0x000055CFDAB54E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000564153234E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [17:55:19] +46: [14:17:37] 46: 46: **** 46: Pre-condition Violation @@ -17421,20 +17356,20 @@ 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::ROMol::addAtom(RDKit::Atom*, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x000055CFDABBB291 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x000055CFDAC07938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x000055CFDAC08458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x000055CFDAC088D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x000055CFDABD9F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x000055CFDABDA2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x000055CFDAB54DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007F2BE3633CA8 in /lib/x86_64-linux-gnu/libc.so.6 +46: 3# 0x000056415329B291 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x00005641532E7938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x00005641532E8458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x00005641532E88D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x00005641532B9F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x00005641532BA2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000564153234DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007F4AFF033CA8 in /lib/x86_64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -46: 12# 0x000055CFDAB54E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000564153234E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [17:55:19] +46: [14:17:37] 46: 46: **** 46: Pre-condition Violation @@ -17446,20 +17381,20 @@ 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::ROMol::addAtom(RDKit::Atom*, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x000055CFDABBAEB8 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x000055CFDAC07938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x000055CFDAC08458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x000055CFDAC088D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x000055CFDABD9F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x000055CFDABDA2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x000055CFDAB54DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007F2BE3633CA8 in /lib/x86_64-linux-gnu/libc.so.6 +46: 3# 0x000056415329AEB8 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x00005641532E7938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x00005641532E8458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x00005641532E88D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x00005641532B9F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x00005641532BA2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000564153234DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007F4AFF033CA8 in /lib/x86_64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -46: 12# 0x000055CFDAB54E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000564153234E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [17:55:19] +46: [14:17:37] 46: 46: **** 46: Pre-condition Violation @@ -17471,24 +17406,24 @@ 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::ROMol::addBond(RDKit::Bond*, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x000055CFDABBB26D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x000055CFDAC07938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x000055CFDAC08458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x000055CFDAC088D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x000055CFDABD9F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x000055CFDABDA2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x000055CFDAB54DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007F2BE3633CA8 in /lib/x86_64-linux-gnu/libc.so.6 +46: 3# 0x000056415329B26D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x00005641532E7938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x00005641532E8458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x00005641532E88D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x00005641532B9F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x00005641532BA2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000564153234DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007F4AFF033CA8 in /lib/x86_64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -46: 12# 0x000055CFDAB54E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000564153234E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [17:55:19] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -46: [17:55:19] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -46: [17:55:19] WARNING: not removing hydrogen atom without neighbors -46: [17:55:19] Explicit valence for atom # 1 F greater than permitted -46: [17:55:19] +46: [14:17:37] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +46: [14:17:37] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +46: [14:17:37] WARNING: not removing hydrogen atom without neighbors +46: [14:17:37] Explicit valence for atom # 1 F greater than permitted +46: [14:17:37] 46: 46: **** 46: Pre-condition Violation @@ -17500,20 +17435,20 @@ 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::Atom::setQuery(Queries::Query*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x000055CFDAB6214B in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x000055CFDAC07938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x000055CFDAC08458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x000055CFDAC088D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x000055CFDABD9F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x000055CFDABDA2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x000055CFDAB54DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007F2BE3633CA8 in /lib/x86_64-linux-gnu/libc.so.6 +46: 3# 0x000056415324214B in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x00005641532E7938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x00005641532E8458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x00005641532E88D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x00005641532B9F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x00005641532BA2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000564153234DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007F4AFF033CA8 in /lib/x86_64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -46: 12# 0x000055CFDAB54E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000564153234E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [17:55:19] +46: [14:17:37] 46: 46: **** 46: Pre-condition Violation @@ -17525,20 +17460,20 @@ 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::Atom::expandQuery(Queries::Query*, Queries::CompositeQueryType, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x000055CFDAB621E0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x000055CFDAC07938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x000055CFDAC08458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x000055CFDAC088D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x000055CFDABD9F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x000055CFDABDA2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x000055CFDAB54DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007F2BE3633CA8 in /lib/x86_64-linux-gnu/libc.so.6 +46: 3# 0x00005641532421E0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x00005641532E7938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x00005641532E8458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x00005641532E88D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x00005641532B9F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x00005641532BA2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000564153234DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007F4AFF033CA8 in /lib/x86_64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -46: 12# 0x000055CFDAB54E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000564153234E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [17:55:19] +46: [14:17:37] 46: 46: **** 46: Pre-condition Violation @@ -17550,20 +17485,20 @@ 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::Bond::setQuery(Queries::Query*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x000055CFDAB61E70 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x000055CFDAC07938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x000055CFDAC08458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x000055CFDAC088D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x000055CFDABD9F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x000055CFDABDA2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x000055CFDAB54DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007F2BE3633CA8 in /lib/x86_64-linux-gnu/libc.so.6 +46: 3# 0x0000564153241E70 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x00005641532E7938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x00005641532E8458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x00005641532E88D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x00005641532B9F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x00005641532BA2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000564153234DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007F4AFF033CA8 in /lib/x86_64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -46: 12# 0x000055CFDAB54E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000564153234E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [17:55:19] +46: [14:17:37] 46: 46: **** 46: Pre-condition Violation @@ -17575,115 +17510,112 @@ 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::Bond::expandQuery(Queries::Query*, Queries::CompositeQueryType, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x000055CFDAB61F05 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x000055CFDAC07938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x000055CFDAC08458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x000055CFDAC088D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x000055CFDABD9F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x000055CFDABDA2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x000055CFDAB54DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007F2BE3633CA8 in /lib/x86_64-linux-gnu/libc.so.6 +46: 3# 0x0000564153241F05 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x00005641532E7938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x00005641532E8458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x00005641532E88D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x00005641532B9F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x00005641532BA2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000564153234DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007F4AFF033CA8 in /lib/x86_64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -46: 12# 0x000055CFDAB54E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000564153234E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [17:55:19] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -46: [17:55:19] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -46: [17:55:19] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -46: [17:55:19] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -46: [17:55:19] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -46: [17:55:19] Unusual charge on atom 0 number of radical electrons set to zero -46: [17:55:19] Unusual charge on atom 0 number of radical electrons set to zero -46: [17:55:19] Unusual charge on atom 0 number of radical electrons set to zero -46: [17:55:19] non-ring atom 0 marked aromatic -46: [17:55:19] non-ring atom 0 marked aromatic -46: [17:55:19] Explicit valence for atom # 1 C, 5, is greater than permitted -46: [17:55:19] Explicit valence for atom # 9 C, 5, is greater than permitted -46: [17:55:19] Explicit valence for atom # 3 N, 4, is greater than permitted -46: [17:55:19] Explicit valence for atom # 15 C, 5, is greater than permitted -46: [17:55:19] Explicit valence for atom # 11 C, 5, is greater than permitted -46: [17:55:19] Explicit valence for atom # 9 C, 5, is greater than permitted -46: [17:55:19] Explicit valence for atom # 9 C, 5, is greater than permitted -46: [17:55:19] Explicit valence for atom # 9 C, 6, is greater than permitted -46: [17:55:19] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -46: [17:55:19] Can't kekulize mol. Unkekulized atoms: 7 -46: [17:55:19] Can't kekulize mol. Unkekulized atoms: 3 -46: [17:55:19] Can't kekulize mol. Unkekulized atoms: 3 7 -46: [17:55:19] Can't kekulize mol. Unkekulized atoms: 3 7 -46: [17:55:19] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -46: [17:55:19] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -47: Randomness seeded to: 2597835332 +46: [14:17:37] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +46: [14:17:37] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +46: [14:17:37] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +46: [14:17:37] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +46: [14:17:37] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +46: [14:17:37] Unusual charge on atom 0 number of radical electrons set to zero +46: [14:17:37] Unusual charge on atom 0 number of radical electrons set to zero +46: [14:17:37] Unusual charge on atom 0 number of radical electrons set to zero +46: [14:17:37] non-ring atom 0 marked aromatic +46: [14:17:37] non-ring atom 0 marked aromatic +46: [14:17:37] Explicit valence for atom # 1 C, 5, is greater than permitted +46: [14:17:37] Explicit valence for atom # 9 C, 5, is greater than permitted +46: [14:17:37] Explicit valence for atom # 3 N, 4, is greater than permitted +46: [14:17:37] Explicit valence for atom # 15 C, 5, is greater than permitted +46: [14:17:37] Explicit valence for atom # 11 C, 5, is greater than permitted +46: [14:17:37] Explicit valence for atom # 9 C, 5, is greater than permitted +46: [14:17:37] Explicit valence for atom # 9 C, 5, is greater than permitted +46: [14:17:37] Explicit valence for atom # 9 C, 6, is greater than permitted +46: [14:17:37] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +46: [14:17:37] Can't kekulize mol. Unkekulized atoms: 7 +46: [14:17:37] Can't kekulize mol. Unkekulized atoms: 3 +46: [14:17:37] Can't kekulize mol. Unkekulized atoms: 3 7 +46: [14:17:37] Can't kekulize mol. Unkekulized atoms: 3 7 +46: [14:17:37] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +46: [14:17:37] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +46: [14:17:37] Explicit valence for atom # 1 O, 3, is greater than permitted +46: [14:17:37] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +46: [14:17:37] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +46: [14:17:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +46: [14:17:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +46: [14:17:37] Invalid value for molAttachPoint: 4 on atom 1. Not expanding this atttachment point. +46: [14:17:37] Invalid value for _fromAttachPoint: -1 on atom 0. Not collapsing this atom +46: [14:17:37] Invalid value for _fromAttachPoint: 4 on atom 0. Not collapsing this atom +46: [14:17:37] non-ring atom 0 marked aromatic +46: [14:17:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +46: [14:17:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +47: Randomness seeded to: 3774448479 47: =============================================================================== 47: All tests passed (62 assertions in 6 test cases) 47: -48: Randomness seeded to: 767090022 +48: Randomness seeded to: 3483995171 48: =============================================================================== 48: All tests passed (136 assertions in 8 test cases) 48: -49: Randomness seeded to: 4293189575 +49: Randomness seeded to: 1239036971 49: =============================================================================== 49: All tests passed (292 assertions in 12 test cases) 49: -50: Randomness seeded to: 667944962 -50: [17:55:19] unable to set wavy bonds for double bonds: 3 -50: [17:55:19] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -50: [17:55:19] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -50: [17:55:19] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. -50: [17:55:19] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. -50: [17:55:19] Warning: ambiguous stereochemistry - overlapping neighbors - at atom 2 ignored +50: Randomness seeded to: 1443165265 +50: [14:17:37] unable to set wavy bonds for double bonds: 3 +50: [14:17:37] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +50: [14:17:37] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +50: [14:17:37] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. +50: [14:17:37] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. +50: [14:17:37] Warning: ambiguous stereochemistry - overlapping neighbors - at atom 2 ignored 50: =============================================================================== 50: All tests passed (2295 assertions in 80 test cases) 50: -52: Randomness seeded to: 3932488488 +52: Randomness seeded to: 1951250457 52: =============================================================================== 52: All tests passed (14 assertions in 4 test cases) 52: -53: Randomness seeded to: 1440944121 +53: Randomness seeded to: 2746637125 53: =============================================================================== 53: All tests passed (10 assertions in 1 test case) 53: -54: Randomness seeded to: 1482937379 +54: Randomness seeded to: 1901382173 54: =============================================================================== 54: All tests passed (6 assertions in 1 test case) 54: -56: Randomness seeded to: 247263151 -56: =============================================================================== -56: All tests passed (7 assertions in 2 test cases) -56: -59: [17:55:19] SMILES Parse Error: Failed parsing SMILES 'CO' for input: 'CO' -59: [17:55:19] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' -59: [17:55:19] SMILES Parse Error: syntax error while parsing: - -59: [17:55:19] SMILES Parse Error: check for mistakes around position 1: -59: [17:55:19] - -59: [17:55:19] ^ -59: [17:55:19] SMILES Parse Error: Failed parsing SMILES '-' for input: '-' -59: [17:55:19] SMILES Parse Error: Failed parsing SMILES '[Bg]' for input: '[Bg]' -59: [17:55:19] SMILES Parse Error: Failed parsing SMILES 'C' for input: 'C' -59: [17:55:19] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' -59: [17:55:19] SMILES Parse Error: Failed parsing SMILES '*' for input: '*' -59: [17:55:19] SMARTS Parse Error: Failed parsing SMARTS 'CO' for input: 'CO' -59: [17:55:19] SMARTS Parse Error: Failed parsing SMARTS 'C-O' for input: 'C-O' -59: [17:55:19] SMARTS Parse Error: Failed parsing SMARTS '-' for input: '-' -59: [17:55:19] SMARTS Parse Error: Failed parsing SMARTS '[Bg]' for input: '[Bg]' -59: [17:55:19] SMARTS Parse Error: Failed parsing SMARTS 'C' for input: 'C' -59: [17:55:19] SMARTS Parse Error: Failed parsing SMARTS '-O' for input: '-O' -59: [17:55:19] SMARTS Parse Error: Failed parsing SMARTS '*' for input: '*' - 24/236 Test #1: testCoordGen ........................... Passed 2.51 sec - 25/236 Test #28: testUFFForceField ...................... Passed 2.46 sec - 26/236 Test #36: graphmoltestChirality .................. Passed 2.45 sec - 27/236 Test #37: graphmoltestPickler .................... Passed 2.45 sec - 28/236 Test #43: molBundleTest .......................... Passed 2.39 sec - 29/236 Test #44: testSGroup ............................. Passed 2.07 sec - 30/236 Test #45: test-valgrind .......................... Passed 2.06 sec - 31/236 Test #47: graphmolOrganometallicsCatch ........... Passed 2.06 sec - 32/236 Test #48: graphmolSGroupCatch .................... Passed 2.05 sec - 33/236 Test #49: graphmolAdjustQueryCatch ............... Passed 2.05 sec - 34/236 Test #52: moliteratorTestsCatch .................. Passed 0.07 sec - 35/236 Test #53: queryTestsCatch ........................ Passed 0.07 sec - 36/236 Test #54: molbundleTestsCatch .................... Passed 0.07 sec - 37/236 Test #56: tableTestsCatch ........................ Passed 0.06 sec - 38/236 Test #59: smiTest2 ............................... Passed 0.05 sec + 25/236 Test #2: pyCoordGen ............................. Passed 1.17 sec + 26/236 Test #13: pyDiscreteValueVect .................... Passed 1.02 sec + 27/236 Test #15: pySparseIntVect ........................ Passed 0.97 sec + 28/236 Test #16: pyFPB .................................. Passed 0.94 sec + 29/236 Test #25: pyAlignment ............................ Passed 0.80 sec + 30/236 Test #32: pyDistGeom ............................. Passed 0.67 sec + 31/236 Test #36: graphmoltestChirality .................. Passed 0.61 sec + 32/236 Test #41: graphmolMemTest1 ....................... Passed 0.45 sec + 33/236 Test #43: molBundleTest .......................... Passed 0.43 sec + 34/236 Test #44: testSGroup ............................. Passed 0.43 sec + 35/236 Test #45: test-valgrind .......................... Passed 0.41 sec + 36/236 Test #47: graphmolOrganometallicsCatch ........... Passed 0.39 sec + 37/236 Test #48: graphmolSGroupCatch .................... Passed 0.38 sec + 38/236 Test #49: graphmolAdjustQueryCatch ............... Passed 0.36 sec + 39/236 Test #52: moliteratorTestsCatch .................. Passed 0.30 sec + 40/236 Test #53: queryTestsCatch ........................ Passed 0.29 sec + 41/236 Test #54: molbundleTestsCatch .................... Passed 0.28 sec +test 65 + Start 65: testDepictor + +65: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/testDepictor +65: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor +65: Test timeout computed to be: 1500 test 66 Start 66: depictorCatch @@ -17774,128 +17706,278 @@ 80: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 80: Test timeout computed to be: 1500 - 39/236 Test #15: pySparseIntVect ........................ Passed 2.66 sec -46: [17:55:19] Explicit valence for atom # 1 O, 3, is greater than permitted -46: [17:55:19] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -46: [17:55:19] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -46: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -46: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -46: [17:55:19] Invalid value for molAttachPoint: 4 on atom 1. Not expanding this atttachment point. -46: [17:55:19] Invalid value for _fromAttachPoint: -1 on atom 0. Not collapsing this atom -46: [17:55:19] Invalid value for _fromAttachPoint: 4 on atom 0. Not collapsing this atom -46: [17:55:19] non-ring atom 0 marked aromatic -46: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -46: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -46: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -46: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -46: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -46: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -46: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored - 40/236 Test #50: chiralityTestsCatch .................... Passed 2.22 sec -55: Randomness seeded to: 439300364 +test 81 + Start 81: testPropertyLists + +81: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testPropertyLists +81: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +81: Test timeout computed to be: 1500 +37: smi match: *CC[OH] *CC[OH] +37: smi match: *=CCC(=O)[OH] *=CCC(=O)[OH] +37: smi match: O=C([OH])CC[OH] O=C([OH])CC[OH] +37: smi match: *CCC(=O)[OH] *CCC(=O)[OH] +37: smi match: CC(=O)CC(=O)[OH] CC(=O)CC(=O)[OH] +37: smi match: *OC(=O)CC(C)=O *OC(=O)CC(C)=O +37: smi match: *OC(*)=O *OC(*)=O +37: smi match: *C(=O)[OH] *C(=O)[OH] +37: smi match: O=C[OH] O=C[OH] +37: smi match: *OC(=O)O* *OC(=O)O* +37: smi match: * * +37: smi match: *OC(=O)Cl *OC(=O)Cl +37: smi match: *C#N *C#N +37: smi match: NCC(=O)NCC=O NCC(=O)NCC=O +37: smi match: SS SS +37: smi match: * * +37: smi match: *=* *=* +37: smi match: *=* *=* +37: smi match: *=* *=* +37: smi match: *=* *=* +37: smi match: C1CO1 C1CO1 +37: smi match: *OC(*)=O *OC(*)=O +37: smi match: * * +37: smi match: *O*[OH] *O*[OH] +37: smi match: COC(C)(C)O COC(C)(C)O +37: smi match: *[OH] *[OH] +37: smi match: ** ** +37: smi match: C=N[NH2] C=N[NH2] +37: smi match: C=NC=O C=NC=O +37: smi match: * * +37: smi match: C#NC C#NC +37: smi match: CN=C=O CN=C=O +37: smi match: CN=C=S CN=C=S +37: smi match: *OC(*)(*)O* *OC(*)(*)O* +37: smi match: *C(*)=O *C(*)=O +37: smi match: C~C~C~C~C~C~C C~C~C~C~C~C~C +37: smi match: *~*=O *~*=O +37: smi match: *~*=O *~*=O +37: smi match: OC(=O)CC(=O)[OH] OC(=O)CC(=O)[OH] +37: smi match: * * +37: smi match: *C#N *C#N +37: smi match: *N(=O)~O *N(=O)~O +37: smi match: N N +37: smi match: OC(=O)C(O)=O OC(=O)C(O)=O +37: smi match: C=NO C=NO +37: smi match: O~O O~O +37: smi match: c[OH] c[OH] +37: smi match: O=P(~[OH])~O O=P(~[OH])~O +37: smi match: CO~P(=O)~O CO~P(=O)~O +37: smi match: O=P(~[OH])(~O)~O O=P(~[OH])(~O)~O +37: smi match: CO~P(=O)(~O)~O CO~P(=O)(~O)~O +37: smi match: O=P(~O)~O O=P(~O)~O +37: smi match: O=P(~O)(~O)~O O=P(~O)(~O)~O +37: smi match: C[NH2] C[NH2] +37: smi match: O~*1~**~*(~O)~**~1 O~*1~**~*(~O)~**~1 +37: smi match: * * +37: smi match: *1~*~*~C2~C(~*~1)~*~*~C1~C3~*~*~*~C~3~*~*~C~2~1 *1~*~*~C2~C(~*~1)~*~*~C1~C3~*~*~*~C~3~*~*~C~2~1 +37: smi match: CS(C)~O CS(C)~O +37: smi match: CS(C)(~O)~O CS(C)(~O)~O +37: smi match: CS(N)(~O)~O CS(N)(~O)~O +37: smi match: CS([OH])(~O)~O CS([OH])(~O)~O +37: smi match: COS(C)(~O)~O COS(C)(~O)~O +37: smi match: *S(C)(~O)~O *S(C)(~O)~O +37: smi match: CN(C)C CN(C)C +37: smi match: *c1nnc(=N)s1 *c1nnc(=N)s1 +37: smi match: *C(*)=S *C(*)=S +37: smi match: *OC(*)=S *OC(*)=S +37: smi match: * * +37: smi match: C[SH] C[SH] +37: smi match: c[SH] c[SH] +37: smi match: NC(N)=S NC(N)=S +37: smi match: * * +37: smi match: ***** ***** +37: smi match: NC(N)=O NC(N)=O +37: [14:17:37] done +37: [14:17:37] ------------------------------------- +37: [14:17:37] Testing sf.net issue 280. +37: [14:17:37] done +37: [14:17:37] ------------------------------------- +37: [14:17:37] Testing sf.net issue 285. +37: [14:17:37] done +37: [14:17:37] done +37: [14:17:37] done +37: [14:17:37] done +37: [14:17:37] done +37: [14:17:37] done +37: [14:17:37] done +37: [14:17:37] ------------------------------------- +37: [14:17:37] Testing Github2441: Add RDProps interface to Conformers. +37: [14:17:37] done +37: [14:17:37] ------------------------------------- +37: [14:17:37] Testing Issue2510: Pickle Confs as double. +37: [14:17:37] done +37: [14:17:37] ------------------------------------- +37: [14:17:37] Testing Github #2465: Negative atom-map numbers cause depickling to fail. +37: [14:17:37] done +37: [14:17:37] ------------------------------------- +37: [14:17:37] Testing loading pickled mols with conformers +37: [14:17:37] done +37: [14:17:37] ------------------------------------- +37: [14:17:37] Testing conformer reading/writing options +37: [14:17:37] done +37: [14:17:37] ------------------------------------- +37: [14:17:37] Testing property reading options +37: [14:17:37] done +37: [14:17:37] ------------------------------------- +37: [14:17:37] Testing property reading options +37: [14:17:37] done +37: [14:17:37] ------------------------------------- +37: [14:17:37] Testing boost::serialization integration +37: [14:17:37] done +37: [14:17:37] ------------------------------------- +37: [14:17:37] Testing github issue 6036 +21: .................... +21: ---------------------------------------------------------------------- +21: Ran 20 tests in 0.229s +21: +21: OK +21: Testing Geometry wrapper +46: [14:17:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +46: [14:17:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +46: [14:17:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +46: [14:17:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +46: [14:17:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +46: [14:17:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +46: [14:17:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +46: [14:17:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +46: [14:17:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +46: [14:17:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +46: [14:17:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +46: [14:17:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. + 42/236 Test #50: chiralityTestsCatch .................... Passed 0.66 sec +56: Randomness seeded to: 4209867801 +56: =============================================================================== +56: All tests passed (7 assertions in 2 test cases) +56: + 43/236 Test #56: tableTestsCatch ........................ Passed 0.55 sec +55: Randomness seeded to: 3905439566 55: =============================================================================== 55: All tests passed (45 assertions in 4 test cases) 55: - 41/236 Test #55: pickleTestsCatch ....................... Passed 0.24 sec -57: Randomness seeded to: 2931532288 + 44/236 Test #55: pickleTestsCatch ....................... Passed 0.57 sec +35: [14:17:37] WARNING: not removing hydrogen atom with dummy atom neighbors +35: ------------------------------- +35: [14:17:37] Explicit valence for atom # 0 N, 4, is greater than permitted +35: [14:17:37] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +35: [14:17:37] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +35: [14:17:37] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +35: [14:17:37] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +35: [14:17:37] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +35: [14:17:37] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +35: [14:17:37] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +35: [14:17:37] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +35: +35: [14:17:37] WARNING: not removing hydrogen atom with dummy atom neighbors +57: Randomness seeded to: 49169036 57: =============================================================================== 57: All tests passed (230 assertions in 7 test cases) 57: - 42/236 Test #57: molopsTestsCatch ....................... Passed 0.23 sec -58: [17:55:19] WARNING: not removing hydrogen atom without neighbors -58: [17:55:19] WARNING: not removing hydrogen atom without neighbors -58: [17:55:19] WARNING: not removing hydrogen atom without neighbors -58: [17:55:19] WARNING: not removing hydrogen atom without neighbors -58: [17:55:19] WARNING: not removing hydrogen atom without neighbors -58: [17:55:19] WARNING: not removing hydrogen atom without neighbors -58: [17:55:19] WARNING: not removing hydrogen atom without neighbors -58: [17:55:19] WARNING: not removing hydrogen atom without neighbors -58: [17:55:19] WARNING: not removing hydrogen atom without neighbors -58: [17:55:19] WARNING: not removing hydrogen atom without neighbors -58: [17:55:19] WARNING: not removing hydrogen atom without neighbors -58: [17:55:19] Invalid chiral specification on atom 0 -58: [17:55:19] Invalid chiral specification on atom 0 -58: [17:55:19] Invalid chiral specification on atom 0 -58: [17:55:19] Invalid chiral specification on atom 0 -58: [17:55:19] Invalid chiral specification on atom 0 -58: [17:55:19] SMILES Parse Error: unclosed ring for input: 'C1.C11.C' -58: [17:55:19] SMILES Parse Error: unclosed ring for input: 'C1C.CC11CCC' -58: --C1CCC2(CC1)CCCCC2CCC1CCCC1 -58: smi: ClC1CCCCC1 -58: smi: ClC1CCCCC1 -58: smi: ClC1CCCCC1Br -58: smi: c1ccccc1 -58: smi: c1ccncc1 -58: smi: c1cc[nH]c1 -58: smi: c1cc[nH]c1 -58: smi: c1cc[pH]c1 -58: [17:55:19] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -58: [17:55:19] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -58: CbC(aC)aC -58: CaC(bC)aC -58: CbC(bC)aC -58: O.C -58: 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 -58: [17:55:19] SMILES Parse Error: syntax error while parsing: c%()ccccc%() -58: [17:55:19] SMILES Parse Error: check for mistakes around position 4: -58: [17:55:19] c%()ccccc%() -58: [17:55:19] ~~~^ -58: [17:55:19] SMILES Parse Error: Failed parsing SMILES 'c%()ccccc%()' for input: 'c%()ccccc%()' -58: [17:55:19] SMILES Parse Error: syntax error while parsing: c%(100000)ccccc%(100000) -58: [17:55:19] SMILES Parse Error: check for mistakes around position 9: -58: [17:55:19] c%(100000)ccccc%(100000) -58: [17:55:19] ~~~~~~~~^ -58: [17:55:19] SMILES Parse Error: Failed parsing SMILES 'c%(100000)ccccc%(100000)' for input: 'c%(100000)ccccc%(100000)' -58: [17:55:19] SMILES Parse Error: duplicated ring closure 1 bonds atom 2 to itself for input: 'C1CC111' -58: [17:55:19] SMILES Parse Error: ring closure 1 duplicates bond between atom 0 and atom 1 for input: 'C1C1' -58: [17:55:19] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -58: [17:55:19] SMILES Parse Error: check for mistakes around position 14: -58: [17:55:19] COc(c1)cccc1C# -58: [17:55:19] ~~~~~~~~~~~~~^ -58: [17:55:19] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -58: [17:55:19] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -58: [17:55:19] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -58: [17:55:19] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -58: [17:55:19] SMILES Parse Error: check for mistakes around position 14: -58: [17:55:19] COc(c1)cccc1C# -58: [17:55:19] ~~~~~~~~~~~~~^ -58: [17:55:19] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -58: [17:55:19] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -58: [17:55:19] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -58: [17:55:19] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -58: [17:55:19] SMILES Parse Error: check for mistakes around position 14: -58: [17:55:19] COc(c1)cccc1C# -58: [17:55:19] ~~~~~~~~~~~~~^ -58: [17:55:19] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -58: [17:55:19] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -58: [17:55:19] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -58: C=c1s/c2n(c1=O)CCCCCCC\N=2 -58: C1=C\C/C=C2C3=C\C/C=C\C=C/C/3C\2\C=C/1 -58: [17:55:19] SMILES Parse Error: extra close parentheses while parsing: C) -58: [17:55:19] SMILES Parse Error: check for mistakes around position 2: -58: [17:55:19] C) -58: [17:55:19] ~^ -58: [17:55:19] SMILES Parse Error: Failed parsing SMILES 'C)' for input: 'C)' -16: ......... -16: ---------------------------------------------------------------------- -16: Ran 9 tests in 0.004s -16: -16: OK -62: Randomness seeded to: 1405504722 -62: [17:55:19] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -62: [17:55:19] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -62: [17:55:19] SMARTS Parse Error: unclosed ring for input: 'c1ccccc' -62: [17:55:19] SMARTS Parse Error: unclosed ring for input: 'C1C' -62: [17:55:19] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -62: [17:55:19] SMARTS Parse Error: syntax error while parsing: C)foo -62: [17:55:19] SMARTS Parse Error: Failed parsing SMARTS 'C)foo' for input: 'C)foo' -62: [17:55:19] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| -62: [17:55:19] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$|' for input: 'CCC |$foo;;bar$|' -62: [17:55:19] unrecognized CXSMILES CONNECT value: 'EU'. Assuming 'eu' -62: [17:55:19] w block attempts to set wedging on bond 0 more than once. -62: [17:55:19] improperly formatted w block -62: [17:55:19] atom 3 is not associated with bond 1(1-2) in w block -62: [17:55:19] + 45/236 Test #57: molopsTestsCatch ....................... Passed 0.54 sec +30: ...[14:17:37] Molecule does not have explicit Hs. Consider calling AddHs() +58: [14:17:37] WARNING: not removing hydrogen atom without neighbors +58: [14:17:37] WARNING: not removing hydrogen atom without neighbors +58: [14:17:37] WARNING: not removing hydrogen atom without neighbors +58: [14:17:37] WARNING: not removing hydrogen atom without neighbors +58: [14:17:37] WARNING: not removing hydrogen atom without neighbors +58: [14:17:37] WARNING: not removing hydrogen atom without neighbors +58: [14:17:37] WARNING: not removing hydrogen atom without neighbors +58: [14:17:37] WARNING: not removing hydrogen atom without neighbors +58: [14:17:37] WARNING: not removing hydrogen atom without neighbors +58: [14:17:37] WARNING: not removing hydrogen atom without neighbors +58: [14:17:37] WARNING: not removing hydrogen atom without neighbors +58: [14:17:37] Invalid chiral specification on atom 0 +58: [14:17:37] Invalid chiral specification on atom 0 +58: [14:17:37] Invalid chiral specification on atom 0 +58: [14:17:37] Invalid chiral specification on atom 0 +58: [14:17:37] Invalid chiral specification on atom 0 +58: [14:17:37] SMILES Parse Error: unclosed ring for input: 'C1.C11.C' +58: [14:17:37] SMILES Parse Error: unclosed ring for input: 'C1C.CC11CCC' +59: [14:17:37] SMILES Parse Error: Failed parsing SMILES 'CO' for input: 'CO' +59: [14:17:37] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' +59: [14:17:37] SMILES Parse Error: syntax error while parsing: - +59: [14:17:37] SMILES Parse Error: check for mistakes around position 1: +59: [14:17:37] - +59: [14:17:37] ^ +59: [14:17:37] SMILES Parse Error: Failed parsing SMILES '-' for input: '-' +59: [14:17:37] SMILES Parse Error: Failed parsing SMILES '[Bg]' for input: '[Bg]' +59: [14:17:37] SMILES Parse Error: Failed parsing SMILES 'C' for input: 'C' +59: [14:17:37] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' +59: [14:17:37] SMILES Parse Error: Failed parsing SMILES '*' for input: '*' +59: [14:17:37] SMARTS Parse Error: Failed parsing SMARTS 'CO' for input: 'CO' +59: [14:17:37] SMARTS Parse Error: Failed parsing SMARTS 'C-O' for input: 'C-O' +59: [14:17:37] SMARTS Parse Error: Failed parsing SMARTS '-' for input: '-' +59: [14:17:37] SMARTS Parse Error: Failed parsing SMARTS '[Bg]' for input: '[Bg]' +59: [14:17:37] SMARTS Parse Error: Failed parsing SMARTS 'C' for input: 'C' +59: [14:17:37] SMARTS Parse Error: Failed parsing SMARTS '-O' for input: '-O' +59: [14:17:37] SMARTS Parse Error: Failed parsing SMARTS '*' for input: '*' + 46/236 Test #59: smiTest2 ............................... Passed 0.48 sec +test 82 + Start 82: XYZFileParserCatchTest + +82: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/XYZFileParserCatchTest +82: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +82: Test timeout computed to be: 1500 +test 83 + Start 83: cdxmlParserCatchTest + +83: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/cdxmlParserCatchTest +83: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +83: Test timeout computed to be: 1500 +test 84 + Start 84: molfileStereoCatchTest + +84: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/molfileStereoCatchTest +84: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +84: Test timeout computed to be: 1500 +test 85 + Start 85: connectTheDotsTest + +85: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/connectTheDotsTest +85: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +85: Test timeout computed to be: 1500 +test 86 + Start 86: v2MolSuppliers + +86: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/v2MolSuppliers +86: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +86: Test timeout computed to be: 1500 +46: [14:17:37] Explicit valence for atom # 0 Al, 6, is greater than permitted +46: [14:17:37] Explicit valence for atom # 0 Al, 6, is greater than permitted +46: [14:17:37] Explicit valence for atom # 1 Si, 6, is greater than permitted +46: [14:17:37] Explicit valence for atom # 1 Si, 6, is greater than permitted +46: [14:17:37] Explicit valence for atom # 0 P, 6, is greater than permitted +46: [14:17:37] Explicit valence for atom # 0 P, 6, is greater than permitted +46: [14:17:37] Explicit valence for atom # 0 P, 7, is greater than permitted +46: [14:17:37] Explicit valence for atom # 0 P, 7, is greater than permitted +46: [14:17:37] Explicit valence for atom # 1 As, 6, is greater than permitted +46: [14:17:37] Explicit valence for atom # 1 As, 6, is greater than permitted +46: [14:17:37] Explicit valence for atom # 1 As, 7, is greater than permitted +46: [14:17:37] Explicit valence for atom # 1 As, 7, is greater than permitted +46: [14:17:37] Explicit valence for atom # 0 Sb, 6, is greater than permitted +46: [14:17:37] Explicit valence for atom # 0 Sb, 6, is greater than permitted +46: [14:17:37] Explicit valence for atom # 0 Sb, 7, is greater than permitted +46: [14:17:37] Explicit valence for atom # 0 Sb, 7, is greater than permitted +46: [14:17:37] Explicit valence for atom # 1 Bi, 6, is greater than permitted +46: [14:17:37] Explicit valence for atom # 1 Bi, 6, is greater than permitted +46: [14:17:37] Explicit valence for atom # 1 Bi, 8, is greater than permitted +46: [14:17:37] Explicit valence for atom # 1 Bi, 8, is greater than permitted +46: =============================================================================== +46: All tests passed (4479 assertions in 107 test cases) +46: +62: Randomness seeded to: 3831390483 +62: [14:17:37] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +62: [14:17:37] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +62: [14:17:37] SMARTS Parse Error: unclosed ring for input: 'c1ccccc' +62: [14:17:37] SMARTS Parse Error: unclosed ring for input: 'C1C' +62: [14:17:37] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +62: [14:17:37] SMARTS Parse Error: syntax error while parsing: C)foo +62: [14:17:37] SMARTS Parse Error: Failed parsing SMARTS 'C)foo' for input: 'C)foo' +62: [14:17:37] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| +62: [14:17:37] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$|' for input: 'CCC |$foo;;bar$|' +62: [14:17:37] unrecognized CXSMILES CONNECT value: 'EU'. Assuming 'eu' +62: [14:17:37] w block attempts to set wedging on bond 0 more than once. +62: [14:17:37] improperly formatted w block +62: [14:17:37] atom 3 is not associated with bond 1(1-2) in w block +62: [14:17:37] 62: 62: **** 62: Range Error @@ -17911,20 +17993,20 @@ 62: 4# RDKit::SmilesWrite::FragmentSmilesConstruct(RDKit::ROMol&, int, std::vector >&, std::vector > const&, RDKit::SmilesWriteParams const&, std::vector >&, std::vector >&, boost::dynamic_bitset > const*, boost::dynamic_bitset > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 62: 5# RDKit::SmilesWrite::detail::MolToSmiles[abi:cxx11](RDKit::ROMol const&, RDKit::SmilesWriteParams const&, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 62: 6# RDKit::MolToSmiles[abi:cxx11](RDKit::ROMol const&, RDKit::SmilesWriteParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 -62: 7# 0x0000559A254F5A5D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 8# 0x0000559A25546D28 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 9# 0x0000559A25547848 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 10# 0x0000559A25547CC0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 11# 0x0000559A25519303 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 12# 0x0000559A2551966C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 13# 0x0000559A254AAE1E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 14# 0x00007FC82F633CA8 in /lib/x86_64-linux-gnu/libc.so.6 +62: 7# 0x000056481E941A5D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 8# 0x000056481E992D28 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 9# 0x000056481E993848 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 10# 0x000056481E993CC0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 11# 0x000056481E965303 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 12# 0x000056481E96566C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 13# 0x000056481E8F6E1E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 14# 0x00007FE60AE33CA8 in /lib/x86_64-linux-gnu/libc.so.6 62: 15# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -62: 16# 0x0000559A254AAE61 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 16# 0x000056481E8F6E61 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch 62: ---------- 62: **** 62: -62: [17:55:19] +62: [14:17:37] 62: 62: **** 62: Range Error @@ -17940,101 +18022,190 @@ 62: 4# RDKit::SmilesWrite::FragmentSmilesConstruct(RDKit::ROMol&, int, std::vector >&, std::vector > const&, RDKit::SmilesWriteParams const&, std::vector >&, std::vector >&, boost::dynamic_bitset > const*, boost::dynamic_bitset > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 62: 5# RDKit::SmilesWrite::detail::MolToSmiles[abi:cxx11](RDKit::ROMol const&, RDKit::SmilesWriteParams const&, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 62: 6# RDKit::MolToSmiles[abi:cxx11](RDKit::ROMol const&, RDKit::SmilesWriteParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 -62: 7# 0x0000559A254F5A5D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 8# 0x0000559A25546D28 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 9# 0x0000559A25547848 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 10# 0x0000559A25547CC0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 11# 0x0000559A25519303 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 12# 0x0000559A2551966C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 13# 0x0000559A254AAE1E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 14# 0x00007FC82F633CA8 in /lib/x86_64-linux-gnu/libc.so.6 +62: 7# 0x000056481E941A5D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 8# 0x000056481E992D28 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 9# 0x000056481E993848 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 10# 0x000056481E993CC0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 11# 0x000056481E965303 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 12# 0x000056481E96566C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 13# 0x000056481E8F6E1E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 14# 0x00007FE60AE33CA8 in /lib/x86_64-linux-gnu/libc.so.6 62: 15# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -62: 16# 0x0000559A254AAE61 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 16# 0x000056481E8F6E61 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch 62: ---------- 62: **** 62: -62: [17:55:19] SMARTS Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5' -62: [17:55:19] SMILES Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5' -62: [17:55:19] SMARTS Parse Error: syntax error while parsing: C1C)foo -62: [17:55:19] SMARTS Parse Error: Failed parsing SMARTS 'C1C)foo' for input: 'C1C)foo' -62: [17:55:19] SMILES Parse Error: extra close parentheses while parsing: C1C)foo -62: [17:55:19] SMILES Parse Error: check for mistakes around position 4: -62: [17:55:19] C1C)foo -62: [17:55:19] ~~~^ -62: [17:55:19] SMILES Parse Error: Failed parsing SMILES 'C1C)foo' for input: 'C1C)foo' -63: Randomness seeded to: 1435971476 -63: [17:55:19] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -63: [17:55:19] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -63: [17:55:19] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -63: [17:55:19] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -63: [17:55:19] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -63: [17:55:19] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -63: [17:55:19] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -63: [17:55:19] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -63: [17:55:19] ignoring non-tetrahedral stereo specification since setAllowNontetrahedralChirality() is false. +62: [14:17:37] SMARTS Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5' +62: [14:17:37] SMILES Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5' +62: [14:17:37] SMARTS Parse Error: syntax error while parsing: C1C)foo +62: [14:17:37] SMARTS Parse Error: Failed parsing SMARTS 'C1C)foo' for input: 'C1C)foo' +62: [14:17:37] SMILES Parse Error: extra close parentheses while parsing: C1C)foo +62: [14:17:37] SMILES Parse Error: check for mistakes around position 4: +62: [14:17:37] C1C)foo +62: [14:17:37] ~~~^ +62: [14:17:37] SMILES Parse Error: Failed parsing SMILES 'C1C)foo' for input: 'C1C)foo' +62: =============================================================================== +62: All tests passed (1588 assertions in 69 test cases) +62: +63: Randomness seeded to: 624479795 +63: [14:17:37] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +63: [14:17:37] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +63: [14:17:37] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +63: [14:17:37] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +63: [14:17:37] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +63: [14:17:37] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +63: [14:17:37] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +63: [14:17:37] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +63: [14:17:37] ignoring non-tetrahedral stereo specification since setAllowNontetrahedralChirality() is false. 63: =============================================================================== 63: All tests passed (308 assertions in 9 test cases) 63: -64: Randomness seeded to: 2646239701 +64: Randomness seeded to: 2157459843 64: =============================================================================== 64: All tests passed (14 assertions in 2 test cases) 64: - 43/236 Test #64: v2smiTestCatch ......................... Passed 0.20 sec -test 81 - Start 81: testPropertyLists +28: done +61: [14:17:37] SMARTS Parse Error: syntax error while parsing: [C:10H3]CC +61: [14:17:37] SMARTS Parse Error: Failed parsing SMARTS '[C:10H3]CC' for input: '[C:10H3]CC' +61: [14:17:37] SMARTS Parse Error: syntax error while parsing: [C:10:3]ON +61: [14:17:37] SMARTS Parse Error: Failed parsing SMARTS '[C:10:3]ON' for input: '[C:10:3]ON' +61: [14:17:37] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +61: [14:17:37] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +66: Randomness seeded to: 1212667591 +66: =============================================================================== +66: All tests passed (580 assertions in 18 test cases) +66: +68: Using new chirality perception +68: Test +68: +68: rxnStereoMarkedCrossed.mrv +68: +68: Test +68: +68: 145323811.mol +68: +68: [14:17:37] unsupported number of radical electrons 5 +69: *************************************** +69: *************************************** +69: [14:17:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [14:17:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [14:17:37] ---- Running with POSIX locale ----- +70: [14:17:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [14:17:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [14:17:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [14:17:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [14:17:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [14:17:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [14:17:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [14:17:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [14:17:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [14:17:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [14:17:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [14:17:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +71: Randomness seeded to: 1961534758 +71: =============================================================================== +71: All tests passed (15 assertions in 3 test cases) +71: +72: [14:17:37] +72: ----------------------------------------- +72: [14:17:37] Ignoring invalid chirality label: '2_bad_chirality' +73: [14:17:37] +73: ----------------------------------------- +73: [14:17:37] Finished: testDetermineFormat() +73: [14:17:37] ----------------------------------------- +73: +73: [14:17:37] +73: ----------------------------------------- +73: [14:17:37] Finished: testSdf() +73: [14:17:37] ----------------------------------------- +73: +73: [14:17:37] +73: ----------------------------------------- +73: [14:17:37] Finished: testSmi() +73: [14:17:37] ----------------------------------------- +73: +73: [14:17:37] +73: ----------------------------------------- +74: [14:17:37] +74: ----------------------------------------- + 47/236 Test #21: testPyGeometry ......................... Passed 1.29 sec + 48/236 Test #28: testUFFForceField ...................... Passed 1.18 sec + 49/236 Test #37: graphmoltestPickler .................... Passed 1.02 sec + 50/236 Test #46: graphmolTestsCatch ..................... Passed 0.83 sec + 51/236 Test #61: smaTest1 ............................... Passed 0.53 sec + 52/236 Test #63: nontetrahedralCatch .................... Passed 0.48 sec + 53/236 Test #64: v2smiTestCatch ......................... Passed 0.47 sec + 54/236 Test #66: depictorCatch .......................... Passed 0.40 sec + 55/236 Test #71: testSquiggleDoubleBonds ................ Passed 0.30 sec + 56/236 Test #76: testTplParser .......................... Passed 0.20 sec +test 87 + Start 87: v2FileParsersCatchTest -81: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testPropertyLists -81: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -81: Test timeout computed to be: 1500 -test 82 - Start 82: XYZFileParserCatchTest +87: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/v2FileParsersCatchTest +87: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +87: Test timeout computed to be: 1500 +test 88 + Start 88: atropisomersCatch -82: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/XYZFileParserCatchTest -82: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -82: Test timeout computed to be: 1500 -test 83 - Start 83: cdxmlParserCatchTest +88: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/atropisomersCatch +88: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +88: Test timeout computed to be: 1500 +test 89 + Start 89: multithreadedSupplierCatchTest -83: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/cdxmlParserCatchTest -83: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -83: Test timeout computed to be: 1500 -test 84 - Start 84: molfileStereoCatchTest +89: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/multithreadedSupplierCatchTest +89: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +89: Test timeout computed to be: 1500 +test 90 + Start 90: testSubstructMatch -84: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/molfileStereoCatchTest -84: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -84: Test timeout computed to be: 1500 -test 85 - Start 85: connectTheDotsTest +90: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct +90: Test timeout computed to be: 1500 +test 91 + Start 91: substructTestCatch -85: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/connectTheDotsTest -85: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -85: Test timeout computed to be: 1500 -13: ...... -13: ---------------------------------------------------------------------- -13: Ran 6 tests in 0.002s -13: -13: OK -35: [17:55:19] Maximum BFS search size exceeded. -35: This is likely due to a highly symmetric fused ring system. -40: [17:55:19] sorting (hanoi sort) vectors -14: ...... -14: ---------------------------------------------------------------------- -14: Ran 6 tests in 0.042s -14: -14: OK -61: [17:55:19] SMARTS Parse Error: syntax error while parsing: [C:10H3]CC -61: [17:55:19] SMARTS Parse Error: Failed parsing SMARTS '[C:10H3]CC' for input: '[C:10H3]CC' -61: [17:55:19] SMARTS Parse Error: syntax error while parsing: [C:10:3]ON -61: [17:55:19] SMARTS Parse Error: Failed parsing SMARTS '[C:10:3]ON' for input: '[C:10:3]ON' -61: [17:55:19] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -61: [17:55:19] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -32: ...... -32: ---------------------------------------------------------------------- -32: Ran 6 tests in 0.001s -32: -32: OK -60: Randomness seeded to: 3430232832 +91: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/substructTestCatch +91: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct +91: Test timeout computed to be: 1500 +test 92 + Start 92: testGenericGroups + +92: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups/testGenericGroups +92: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups +92: Test timeout computed to be: 1500 +test 93 + Start 93: testReaction + +93: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/testReaction +93: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions +93: Test timeout computed to be: 1500 +test 94 + Start 94: testReactionFingerprints + +94: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/testReactionFingerprints +94: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions +94: Test timeout computed to be: 1500 +test 95 + Start 95: testEnumeration + +95: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/testEnumeration +95: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions +95: Test timeout computed to be: 1500 +test 96 + Start 96: rxnTestCatch + +96: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/rxnTestCatch +96: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions +96: Test timeout computed to be: 1500 + 57/236 Test #62: smiTestCatch ........................... Passed 0.65 sec +30: ......[14:17:37] Molecule does not have explicit Hs. Consider calling AddHs() +30: ... +30: ---------------------------------------------------------------------- +30: Ran 12 tests in 0.749s +30: +30: OK +60: Randomness seeded to: 789969846 60: Test 60: 60: ShortAtropisomerNoCoords.cxsmi @@ -18095,16 +18266,16 @@ 60: 60: BMS-986142_atrop5.cxsmi 60: -60: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [14:17:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [14:17:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [14:17:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [14:17:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [14:17:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [14:17:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [14:17:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [14:17:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [14:17:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [14:17:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 60: Test 60: 60: BMS-986142_atrop6.cxsmi @@ -18113,180 +18284,25 @@ 60: 60: BMS-986142_atropBad1.cxsmi 60: -60: [17:55:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -60: [17:55:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -60: [17:55:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -60: [17:55:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -60: [17:55:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +60: [14:17:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +60: [14:17:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +60: [14:17:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +60: [14:17:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +60: [14:17:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 60: Test 60: 60: BMS-986142_atropBad2.cxsmi 60: -60: [17:55:19] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -60: [17:55:19] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -60: [17:55:19] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -60: [17:55:19] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -60: [17:55:19] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -60: Test -60: -60: JDQ443_3d.cxsmi -60: -60: Test -60: -60: JDQ443_atrop1.cxsmi -60: -60: Test -60: -60: JDQ443_atrop2.cxsmi -60: -60: Test -60: -60: JDQ443_atrop3.cxsmi -60: -60: Test -60: -60: JDQ443_atrop4.cxsmi -60: -60: Test -60: -60: JDQ443_atropBad1.cxsmi -60: -60: [17:55:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -60: [17:55:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -60: [17:55:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -60: [17:55:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -60: [17:55:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -66: Randomness seeded to: 3389208062 -66: =============================================================================== -66: All tests passed (580 assertions in 18 test cases) -66: -68: Using new chirality perception -68: Test -68: -68: rxnStereoMarkedCrossed.mrv -68: -68: Test -68: -68: 145323811.mol -68: -68: [17:55:19] unsupported number of radical electrons 5 -68: Test -68: -68: NewChiralTest.sdf -68: -68: Test -68: -68: NewChiralTest.sdf -68: -68: Test -68: -68: NewChiralTestNoChiral.sdf -68: -68: Test -68: -68: NewChiralTestNoChiral.sdf -68: -68: Test -68: -68: NewChiralTestAllChiral.sdf -68: -68: Test -68: -68: NewChiralTestAllChiral.sdf -68: -68: Test -68: -68: vendor839.sdf -68: -68: Test -68: -68: ProblemShort.mol -68: -68: [17:55:19] For a MultipleSgroup expansion, the matching orphaned bond was not found -68: The multiple sgroup will be ignored -69: *************************************** -69: *************************************** -69: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: [17:55:19] bond with order 0 found on line 7. This is not part of the MDL specification. -70: [17:55:19] ---- Running with POSIX locale ----- -70: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [17:55:19] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 -70: [17:55:19] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 -70: [17:55:19] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 -70: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -71: Randomness seeded to: 3009090437 -71: =============================================================================== -71: All tests passed (15 assertions in 3 test cases) -71: -72: [17:55:19] -72: ----------------------------------------- -72: [17:55:19] Ignoring invalid chirality label: '2_bad_chirality' -72: [17:55:19] Finished: testMolSup() -72: [17:55:19] ----------------------------------------- -72: -72: [17:55:19] ----------------------------------------- -72: [17:55:19] Finished: testRandMolSup() -72: [17:55:19] ----------------------------------------- -72: -72: [17:55:19] ----------------------------------------- -72: [17:55:19] Finished: testSmilesSup() -72: [17:55:19] ----------------------------------------- -72: -72: [17:55:19] ----------------------------------------- -72: [17:55:19] ------------------------------------------------------ -72: [17:55:19] SMILES Parse Error: syntax error while parsing: fail -72: [17:55:19] SMILES Parse Error: check for mistakes around position 1: -72: [17:55:19] fail -72: [17:55:19] ^ -72: [17:55:19] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' -72: [17:55:19] ERROR: Smiles parse error on line 3 -72: [17:55:19] ERROR: Cannot create molecule from : 'fail' -72: [17:55:19] ------------------------------------------------------ -72: [17:55:19] ------------------------------------------------------ -72: [17:55:19] >>> This may result in an infinite loop. It should finish almost immediately: -72: [17:55:19] <<< done. -72: [17:55:19] Finished: testSmilesSupFromText() -72: [17:55:19] ----------------------------------------- -72: -72: [17:55:19] ----------------------------------------- -73: [17:55:19] -73: ----------------------------------------- -73: [17:55:19] Finished: testDetermineFormat() -73: [17:55:19] ----------------------------------------- -73: -73: [17:55:19] -73: ----------------------------------------- -73: [17:55:19] Finished: testSdf() -73: [17:55:19] ----------------------------------------- -73: -73: [17:55:19] -73: ----------------------------------------- -73: [17:55:19] Finished: testSmi() -73: [17:55:19] ----------------------------------------- -73: -73: [17:55:19] -73: ----------------------------------------- -74: [17:55:19] -74: ----------------------------------------- +60: [14:17:38] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +60: [14:17:38] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +60: [14:17:38] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +60: [14:17:38] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +60: [14:17:38] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +81: Randomness seeded to: 2959586508 +81: =============================================================================== +81: All tests passed (95 assertions in 4 test cases) +81: + 58/236 Test #81: testPropertyLists ...................... Passed 0.29 sec 78: Sequence: GREG 78: HELM: PEPTIDE1{G.R.E.G}$$$$ 78: Smiles: N=C(N)NCCC[C@H](NC(=O)CN)C(=O)N[C@@H](CCC(=O)O)C(=O)NCC(=O)O @@ -19271,319 +19287,29 @@ 78: CONECT 27 28 28 29 78: END 78: - 44/236 Test #13: pyDiscreteValueVect .................... Passed 2.69 sec - 45/236 Test #14: pyRealValueVect ........................ Passed 2.69 sec - 46/236 Test #16: pyFPB .................................. Passed 2.69 sec - 47/236 Test #32: pyDistGeom ............................. Passed 2.66 sec - 48/236 Test #58: smiTest1 ............................... Passed 0.26 sec - 49/236 Test #61: smaTest1 ............................... Passed 0.24 sec - 50/236 Test #63: nontetrahedralCatch .................... Passed 0.23 sec - 51/236 Test #66: depictorCatch .......................... Passed 0.20 sec - 52/236 Test #71: testSquiggleDoubleBonds ................ Passed 0.19 sec - 53/236 Test #76: testTplParser .......................... Passed 0.18 sec - 54/236 Test #78: testSequence ........................... Passed 0.12 sec - 55/236 Test #79: testExtendedStereoParsing .............. Passed 0.11 sec -test 86 - Start 86: v2MolSuppliers - -86: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/v2MolSuppliers -86: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -86: Test timeout computed to be: 1500 -test 87 - Start 87: v2FileParsersCatchTest - -87: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/v2FileParsersCatchTest -87: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -87: Test timeout computed to be: 1500 -test 88 - Start 88: atropisomersCatch - -88: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/atropisomersCatch -88: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -88: Test timeout computed to be: 1500 -test 89 - Start 89: multithreadedSupplierCatchTest - -89: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/multithreadedSupplierCatchTest -89: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -89: Test timeout computed to be: 1500 -test 90 - Start 90: testSubstructMatch - -90: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -90: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct -90: Test timeout computed to be: 1500 -test 91 - Start 91: substructTestCatch - -91: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/substructTestCatch -91: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct -91: Test timeout computed to be: 1500 -test 92 - Start 92: testGenericGroups - -92: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups/testGenericGroups -92: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups -92: Test timeout computed to be: 1500 -test 93 - Start 93: testReaction - -93: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/testReaction -93: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions -93: Test timeout computed to be: 1500 -test 94 - Start 94: testReactionFingerprints - -94: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/testReactionFingerprints -94: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions -94: Test timeout computed to be: 1500 -test 95 - Start 95: testEnumeration - -95: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/testEnumeration -95: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions -95: Test timeout computed to be: 1500 -test 96 - Start 96: rxnTestCatch - -96: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/rxnTestCatch -96: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions -96: Test timeout computed to be: 1500 -test 97 - Start 97: pyChemReactions - -97: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py" -97: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap -97: Test timeout computed to be: 1500 -60: Test -60: -60: RP-6306_atrop1.cxsmi -60: -60: Test -60: -60: RP-6306_atrop2.cxsmi -60: -60: Test -60: -60: RP-6306_atrop3.cxsmi -60: -60: Test -60: -60: RP-6306_atrop4.cxsmi -60: -60: Test -60: -60: RP-6306_atrop5.cxsmi -60: -60: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: Test -60: -60: RP-6306_atrop6.cxsmi -60: -60: Test -60: -60: RP-6306_atropBad1.cxsmi -60: -60: [17:55:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -60: [17:55:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -60: [17:55:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -60: [17:55:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -60: [17:55:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -60: Test -60: -60: RP-6306_atropBad2.cxsmi -60: -60: [17:55:19] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -60: [17:55:19] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -60: [17:55:19] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -60: [17:55:19] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -60: [17:55:19] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -70: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [17:55:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 -70: [17:55:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 -70: [17:55:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 -70: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [17:55:19] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 -70: [17:55:19] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 -70: [17:55:19] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 -70: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [17:55:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -70: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [17:55:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -70: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [17:55:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -70: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -72: [17:55:19] Finished: testSmilesWriter() -72: [17:55:19] ----------------------------------------- -72: -72: [17:55:19] ----------------------------------------- -72: [17:55:19] Finished: testSDWriter() -72: [17:55:19] ----------------------------------------- -72: -72: [17:55:19] ----------------------------------------- -72: [17:55:19] Finished: testSDSupplierEnding() -72: [17:55:19] ----------------------------------------- -72: -72: [17:55:19] ----------------------------------------- -72: [17:55:19] Finished: testSuppliersEmptyFile() -72: [17:55:19] ----------------------------------------- -72: -72: [17:55:19] ----------------------------------------- -72: [17:55:19] Finished: testCisTrans() -72: [17:55:19] ----------------------------------------- -72: -72: [17:55:19] ----------------------------------------- -72: [17:55:19] Finished: testStereoRound() -72: [17:55:19] ----------------------------------------- -72: -72: [17:55:19] ----------------------------------------- -72: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -72: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -72: [17:55:19] Finished: testIssue226() -72: [17:55:19] ----------------------------------------- -72: -72: [17:55:19] ----------------------------------------- -72: [17:55:19] Finished: testTDTSupplier1() -72: [17:55:19] ----------------------------------------- -72: -72: [17:55:19] ----------------------------------------- -72: [17:55:19] Finished: testTDTSupplier2() -72: [17:55:19] ----------------------------------------- -72: -72: [17:55:19] ----------------------------------------- -72: [17:55:19] Finished: testTDTSupplier3() -72: [17:55:19] ----------------------------------------- -72: -72: [17:55:19] ----------------------------------------- -72: [17:55:19] Finished: testSDSupplierFromText() -72: [17:55:19] ----------------------------------------- -72: -72: [17:55:19] ----------------------------------------- -72: [17:55:19] ERROR: Problems encountered parsing data fields -72: [17:55:19] ERROR: moving to the beginning of the next molecule -72: [17:55:19] ERROR: Problems encountered parsing data fields -72: [17:55:19] ERROR: moving to the beginning of the next molecule -72: [17:55:19] Spurious data before the first property will be ignored -72: [17:55:19] Property will be truncated after the first blank line -72: [17:55:19] Property will be truncated after the first blank line -72: [17:55:19] Property will be truncated after the first blank line -72: [17:55:19] Finished: testSDSupplierStrLax1() -72: [17:55:19] ----------------------------------------- -72: -72: [17:55:19] ----------------------------------------- -72: [17:55:19] ERROR: Problems encountered parsing data fields -72: [17:55:19] ERROR: moving to the beginning of the next molecule -72: [17:55:19] Property will be truncated after the first blank line -72: [17:55:19] Finished: testSDSupplierStrLax2() -72: [17:55:19] ----------------------------------------- -72: -72: [17:55:19] ----------------------------------------- -72: [17:55:19] ERROR: Problems encountered parsing data fields -72: [17:55:19] ERROR: moving to the beginning of the next molecule -72: [17:55:19] ERROR: Problems encountered parsing data fields -72: [17:55:19] ERROR: moving to the beginning of the next molecule -72: [17:55:19] Spurious data before the first property will be ignored -72: [17:55:19] Property will be truncated after the first blank line -72: [17:55:19] Property will be truncated after the first blank line -72: [17:55:19] Property will be truncated after the first blank line -72: [17:55:19] Finished: testSDSupplierFromTextStrLax1() -72: [17:55:19] ----------------------------------------- -72: -72: [17:55:19] ----------------------------------------- -72: [17:55:19] ERROR: Problems encountered parsing data fields -72: [17:55:19] ERROR: moving to the beginning of the next molecule -72: [17:55:19] Property will be truncated after the first blank line -72: [17:55:19] Finished: testSDSupplierFromTextStrLax2() -72: [17:55:19] ----------------------------------------- -72: -72: [17:55:19] ----------------------------------------- -72: [17:55:19] Finished: testIssue265() -72: [17:55:19] ----------------------------------------- -72: -72: [17:55:19] ----------------------------------------- -72: [17:55:19] ERROR: End of data field name not found -72: [17:55:19] ERROR: moving to the beginning of the next molecule -72: [17:55:19] Explicit valence for atom # 0 F, 2, is greater than permitted -72: [17:55:19] ERROR: Could not sanitize molecule ending on line 16 -72: [17:55:19] ERROR: Explicit valence for atom # 0 F, 2, is greater than permitted -72: [17:55:19] ERROR: Atom line too short: ' 1 2 1 0 0 0 0' on line 12 -72: [17:55:19] ERROR: moving to the beginning of the next molecule -72: [17:55:19] ERROR: Bond line too short: 'M END' on line 18 -72: [17:55:19] ERROR: moving to the beginning of the next molecule -72: [17:55:19] Finished: testSDErrorHandling() -72: [17:55:19] ----------------------------------------- -72: -72: [17:55:19] ----------------------------------------- -72: [17:55:19] Finished: testIssue381() -72: [17:55:19] ----------------------------------------- -72: -72: [17:55:19] ----------------------------------------- -72: [17:55:19] Finished: testSetStreamIndices() -72: [17:55:19] ----------------------------------------- -72: -72: [17:55:19] ----------------------------------------- -62: =============================================================================== -62: All tests passed (1588 assertions in 69 test cases) -62: - 56/236 Test #62: smiTestCatch ........................... Passed 0.28 sec -46: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -46: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -46: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -46: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -46: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -46: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 57/236 Test #77: testMol2ToMol .......................... Passed 0.22 sec -25: ..... -25: ---------------------------------------------------------------------- -25: Ran 5 tests in 0.002s -25: -25: OK -25: Testing Alignment Wrapper code: -80: Randomness seeded to: 3294963954 -80: [17:55:19] SGroup SAP line too short: 'M SAP 1 1 8' on line 29 -80: [17:55:19] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 -80: [17:55:19] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -80: [17:55:19] SGroup 1 is invalid and will be ignored -80: [17:55:19] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 -80: [17:55:19] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -80: [17:55:19] SGroup 1 is invalid and will be ignored -80: [17:55:19] SGroup SAP line too short: 'M SAP 1 1 8' on line 35 -80: [17:55:19] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 -80: [17:55:19] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 -80: [17:55:19] SGroup SAP line too short: 'M SAP 2 1 12' on line 38 -80: [17:55:19] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -80: [17:55:19] SGroup 1 is invalid and will be ignored -80: [17:55:19] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 -80: [17:55:19] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 -80: [17:55:19] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -80: [17:55:19] SGroup 1 is invalid and will be ignored -80: [17:55:19] SGroup 3 referenced on line 40 not found. -80: [17:55:19] + 59/236 Test #78: testSequence ........................... Passed 0.40 sec + 60/236 Test #77: testMol2ToMol .......................... Passed 0.41 sec + 61/236 Test #79: testExtendedStereoParsing .............. Passed 0.38 sec +80: Randomness seeded to: 495247451 +80: [14:17:37] SGroup SAP line too short: 'M SAP 1 1 8' on line 29 +80: [14:17:37] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 +80: [14:17:37] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +80: [14:17:37] SGroup 1 is invalid and will be ignored +80: [14:17:37] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 +80: [14:17:37] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +80: [14:17:37] SGroup 1 is invalid and will be ignored +80: [14:17:37] SGroup SAP line too short: 'M SAP 1 1 8' on line 35 +80: [14:17:37] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 +80: [14:17:37] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 +80: [14:17:37] SGroup SAP line too short: 'M SAP 2 1 12' on line 38 +80: [14:17:37] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +80: [14:17:37] SGroup 1 is invalid and will be ignored +80: [14:17:37] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 +80: [14:17:37] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 +80: [14:17:37] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +80: [14:17:37] SGroup 1 is invalid and will be ignored +80: [14:17:37] SGroup 3 referenced on line 40 not found. +80: [14:17:37] 80: 80: **** 80: Pre-condition Violation @@ -19596,24 +19322,24 @@ 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::SubstanceGroup::addCState(unsigned int, RDGeom::Point3D const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 3# RDKit::SGroupParsing::ParseSGroupV2000SBVLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 4# 0x00007FF988CDA81E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 4# 0x00007FBDC4CDA81E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 5# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 6# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 7# 0x0000561A06AA06A9 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x0000561A06B18228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000561A06B18D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000561A06B191C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000561A06AEA8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000561A06AEAC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000561A06A5DC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x00007FF988233CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 7# 0x000055D8E67396A9 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x000055D8E67B1228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x000055D8E67B1D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x000055D8E67B21C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x000055D8E67838C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x000055D8E6783C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x000055D8E66F6C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x00007FBDC4233CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 15# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 16# 0x0000561A06A5DC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x000055D8E66F6C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [17:55:19] SGroup 3 referenced on line 40 not found. -80: [17:55:19] +80: [14:17:37] SGroup 3 referenced on line 40 not found. +80: [14:17:37] 80: 80: **** 80: Pre-condition Violation @@ -19626,29 +19352,29 @@ 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::SubstanceGroup::addCState(unsigned int, RDGeom::Point3D const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 3# RDKit::SGroupParsing::ParseSGroupV2000SBVLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 4# 0x00007FF988CDA81E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 4# 0x00007FBDC4CDA81E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 5# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 6# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 7# 0x0000561A06AA0752 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x0000561A06B18228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000561A06B18D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000561A06B191C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000561A06AEA8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000561A06AEAC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000561A06A5DC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x00007FF988233CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 7# 0x000055D8E6739752 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x000055D8E67B1228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x000055D8E67B1D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x000055D8E67B21C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x000055D8E67838C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x000055D8E6783C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x000055D8E66F6C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x00007FBDC4233CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 15# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 16# 0x0000561A06A5DC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x000055D8E66F6C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [17:55:19] no bonds -80: [17:55:19] SGroup 1 is invalid and will be ignored -80: [17:55:19] SGroup line too short: 'M SBV 1 6' on line 42 -80: [17:55:19] SGroup 1 is invalid and will be ignored -80: [17:55:19] SGroup line too short: 'M SBL 2 3 9 10' on line 46 -80: [17:55:19] SGroup 2 is invalid and will be ignored -80: [17:55:19] +80: [14:17:37] no bonds +80: [14:17:37] SGroup 1 is invalid and will be ignored +80: [14:17:37] SGroup line too short: 'M SBV 1 6' on line 42 +80: [14:17:37] SGroup 1 is invalid and will be ignored +80: [14:17:37] SGroup line too short: 'M SBL 2 3 9 10' on line 46 +80: [14:17:37] SGroup 2 is invalid and will be ignored +80: [14:17:37] 80: 80: **** 80: Pre-condition Violation @@ -19662,23 +19388,23 @@ 80: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 4# RDKit::SGroupParsing::ParseSGroupV2000VectorDataLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# 0x00007FF988CDA6AB in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x00007FBDC4CDA6AB in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 8# 0x0000561A06AA1312 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000561A06B18228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000561A06B18D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000561A06B191C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000561A06AEA8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000561A06AEAC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000561A06A5DC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x00007FF988233CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 8# 0x000055D8E673A312 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x000055D8E67B1228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x000055D8E67B1D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x000055D8E67B21C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x000055D8E67838C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x000055D8E6783C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x000055D8E66F6C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x00007FBDC4233CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 17# 0x0000561A06A5DC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 17# 0x000055D8E66F6C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [17:55:19] +80: [14:17:37] 80: 80: **** 80: Pre-condition Violation @@ -19692,24 +19418,24 @@ 80: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 4# RDKit::SGroupParsing::ParseSGroupV2000VectorDataLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# 0x00007FF988CDA6AB in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x00007FBDC4CDA6AB in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 8# 0x0000561A06AA13BA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000561A06B18228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000561A06B18D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000561A06B191C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000561A06AEA8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000561A06AEAC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000561A06A5DC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x00007FF988233CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 8# 0x000055D8E673A3BA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x000055D8E67B1228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x000055D8E67B1D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x000055D8E67B21C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x000055D8E67838C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x000055D8E6783C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x000055D8E66F6C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x00007FBDC4233CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 17# 0x0000561A06A5DC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 17# 0x000055D8E66F6C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [17:55:19] bookmark not found -80: [17:55:19] +80: [14:17:37] bookmark not found +80: [14:17:37] 80: 80: **** 80: Pre-condition Violation @@ -19723,25 +19449,25 @@ 80: 2# RDKit::SubstanceGroup::getBondType(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 3# RDKit::SubstanceGroup::addCState(unsigned int, RDGeom::Point3D const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 4# RDKit::SGroupParsing::ParseSGroupV2000SBVLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# 0x00007FF988CDA81E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x00007FBDC4CDA81E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 8# 0x0000561A06AA13BA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000561A06B18228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000561A06B18D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000561A06B191C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000561A06AEA8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000561A06AEAC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000561A06A5DC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x00007FF988233CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 8# 0x000055D8E673A3BA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x000055D8E67B1228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x000055D8E67B1D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x000055D8E67B21C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x000055D8E67838C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x000055D8E6783C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x000055D8E66F6C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x00007FBDC4233CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 17# 0x0000561A06A5DC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 17# 0x000055D8E66F6C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [17:55:19] bond is not part of the SubstanceGroup -80: [17:55:19] SGroup 2 is invalid and will be ignored -80: [17:55:19] +80: [14:17:37] bond is not part of the SubstanceGroup +80: [14:17:37] SGroup 2 is invalid and will be ignored +80: [14:17:37] 80: 80: **** 80: Pre-condition Violation @@ -19755,23 +19481,23 @@ 80: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 4# RDKit::SGroupParsing::ParseSGroupV2000VectorDataLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# 0x00007FF988CDA6AB in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x00007FBDC4CDA6AB in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 8# 0x0000561A06AA1729 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000561A06B18228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000561A06B18D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000561A06B191C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000561A06AEA8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000561A06AEAC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000561A06A5DC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x00007FF988233CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 8# 0x000055D8E673A729 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x000055D8E67B1228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x000055D8E67B1D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x000055D8E67B21C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x000055D8E67838C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x000055D8E6783C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x000055D8E66F6C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x00007FBDC4233CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 17# 0x0000561A06A5DC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 17# 0x000055D8E66F6C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [17:55:19] +80: [14:17:37] 80: 80: **** 80: Pre-condition Violation @@ -19785,27 +19511,27 @@ 80: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 4# RDKit::SGroupParsing::ParseSGroupV2000VectorDataLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# 0x00007FF988CDA6AB in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x00007FBDC4CDA6AB in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 8# 0x0000561A06AA17D1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000561A06B18228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000561A06B18D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000561A06B191C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000561A06AEA8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000561A06AEAC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000561A06A5DC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x00007FF988233CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 8# 0x000055D8E673A7D1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x000055D8E67B1228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x000055D8E67B1D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x000055D8E67B21C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x000055D8E67838C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x000055D8E6783C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x000055D8E66F6C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x00007FBDC4233CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 17# 0x0000561A06A5DC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 17# 0x000055D8E66F6C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [17:55:19] bookmark not found -80: [17:55:19] Neither beginning nor ending atoms of bond 9 is in this SubstanceGroup. -80: [17:55:19] SGroup 2 is invalid and will be ignored -80: [17:55:19] WARNING: final character of V3000 array is not ')' -80: [17:55:19] +80: [14:17:38] bookmark not found +80: [14:17:38] Neither beginning nor ending atoms of bond 9 is in this SubstanceGroup. +80: [14:17:38] SGroup 2 is invalid and will be ignored +80: [14:17:38] WARNING: final character of V3000 array is not ')' +80: [14:17:38] 80: 80: **** 80: Pre-condition Violation @@ -19823,21 +19549,21 @@ 80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 9# 0x0000561A06A9F033 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000561A06B18228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000561A06B18D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000561A06B191C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000561A06AEA8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000561A06AEAC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000561A06A5DC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x00007FF988233CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 9# 0x000055D8E6738033 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x000055D8E67B1228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x000055D8E67B1D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x000055D8E67B21C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x000055D8E67838C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x000055D8E6783C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x000055D8E66F6C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x00007FBDC4233CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 18# 0x0000561A06A5DC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x000055D8E66F6C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [17:55:19] WARNING: final character of V3000 array is not ')' -80: [17:55:19] +80: [14:17:38] WARNING: final character of V3000 array is not ')' +80: [14:17:38] 80: 80: **** 80: Pre-condition Violation @@ -19855,23 +19581,23 @@ 80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 9# 0x0000561A06A9F0CB in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000561A06B18228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000561A06B18D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000561A06B191C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000561A06AEA8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000561A06AEAC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000561A06A5DC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x00007FF988233CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 9# 0x000055D8E67380CB in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x000055D8E67B1228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x000055D8E67B1D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x000055D8E67B21C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x000055D8E67838C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x000055D8E6783C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x000055D8E66F6C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x00007FBDC4233CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 18# 0x0000561A06A5DC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x000055D8E66F6C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [17:55:19] bookmark not found -80: [17:55:19] SGroup 1 is invalid and will be ignored -80: [17:55:19] WARNING: final character of V3000 array is not ')' -80: [17:55:19] +80: [14:17:38] bookmark not found +80: [14:17:38] SGroup 1 is invalid and will be ignored +80: [14:17:38] WARNING: final character of V3000 array is not ')' +80: [14:17:38] 80: 80: **** 80: Pre-condition Violation @@ -19889,21 +19615,21 @@ 80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 9# 0x0000561A06A9F434 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000561A06B18228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000561A06B18D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000561A06B191C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000561A06AEA8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000561A06AEAC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000561A06A5DC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x00007FF988233CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 9# 0x000055D8E6738434 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x000055D8E67B1228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x000055D8E67B1D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x000055D8E67B21C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x000055D8E67838C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x000055D8E6783C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x000055D8E66F6C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x00007FBDC4233CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 18# 0x0000561A06A5DC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x000055D8E66F6C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [17:55:19] WARNING: final character of V3000 array is not ')' -80: [17:55:19] +80: [14:17:38] WARNING: final character of V3000 array is not ')' +80: [14:17:38] 80: 80: **** 80: Pre-condition Violation @@ -19921,22 +19647,22 @@ 80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 9# 0x0000561A06A9F4CC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000561A06B18228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000561A06B18D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000561A06B191C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000561A06AEA8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000561A06AEAC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000561A06A5DC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x00007FF988233CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 9# 0x000055D8E67384CC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x000055D8E67B1228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x000055D8E67B1D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x000055D8E67B21C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x000055D8E67838C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x000055D8E6783C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x000055D8E66F6C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x00007FBDC4233CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 18# 0x0000561A06A5DC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x000055D8E66F6C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [17:55:19] bookmark not found -80: [17:55:19] SGroup 1 is invalid and will be ignored -80: [17:55:19] +80: [14:17:38] bookmark not found +80: [14:17:38] SGroup 1 is invalid and will be ignored +80: [14:17:38] 80: 80: **** 80: Pre-condition Violation @@ -19954,20 +19680,20 @@ 80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 9# 0x0000561A06A9F833 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000561A06B18228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000561A06B18D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000561A06B191C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000561A06AEA8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000561A06AEAC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000561A06A5DC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x00007FF988233CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 9# 0x000055D8E6738833 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x000055D8E67B1228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x000055D8E67B1D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x000055D8E67B21C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x000055D8E67838C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x000055D8E6783C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x000055D8E66F6C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x00007FBDC4233CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 18# 0x0000561A06A5DC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x000055D8E66F6C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [17:55:19] +80: [14:17:38] 80: 80: **** 80: Pre-condition Violation @@ -19985,22 +19711,22 @@ 80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 9# 0x0000561A06A9F8CC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000561A06B18228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000561A06B18D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000561A06B191C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000561A06AEA8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000561A06AEAC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000561A06A5DC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x00007FF988233CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 9# 0x000055D8E67388CC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x000055D8E67B1228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x000055D8E67B1D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x000055D8E67B21C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x000055D8E67838C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x000055D8E6783C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x000055D8E66F6C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x00007FBDC4233CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 18# 0x0000561A06A5DC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x000055D8E66F6C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [17:55:19] bookmark not found -80: [17:55:19] SGroup 2 is invalid and will be ignored -80: [17:55:19] +80: [14:17:38] bookmark not found +80: [14:17:38] SGroup 2 is invalid and will be ignored +80: [14:17:38] 80: 80: **** 80: Pre-condition Violation @@ -20018,20 +19744,20 @@ 80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 9# 0x0000561A06A9FC32 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000561A06B18228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000561A06B18D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000561A06B191C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000561A06AEA8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000561A06AEAC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000561A06A5DC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x00007FF988233CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 9# 0x000055D8E6738C32 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x000055D8E67B1228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x000055D8E67B1D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x000055D8E67B21C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x000055D8E67838C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x000055D8E6783C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x000055D8E66F6C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x00007FBDC4233CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 18# 0x0000561A06A5DC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x000055D8E66F6C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [17:55:19] +80: [14:17:38] 80: 80: **** 80: Pre-condition Violation @@ -20049,146 +19775,30 @@ 80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 9# 0x0000561A06A9FCCC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000561A06B18228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000561A06B18D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000561A06B191C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000561A06AEA8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000561A06AEAC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000561A06A5DC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x00007FF988233CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 9# 0x000055D8E6738CCC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x000055D8E67B1228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x000055D8E67B1D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x000055D8E67B21C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x000055D8E67838C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x000055D8E6783C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x000055D8E66F6C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x00007FBDC4233CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 18# 0x0000561A06A5DC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x000055D8E66F6C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [17:55:19] bookmark not found -80: [17:55:19] SGroup 2 is invalid and will be ignored -80: [17:55:19] Explicit valence for atom # 2 O, 3, is greater than permitted -80: [17:55:19] Explicit valence for atom # 1 O, 3, is greater than permitted -80: [17:55:19] Explicit valence for atom # 1 C, 5, is greater than permitted -80: [17:55:19] sanitize [17:55:19] UNK: [17:55:19] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -80: [17:55:19] skipping block at line 7: 'BEGIN ATOM' +80: [14:17:38] bookmark not found +80: [14:17:38] SGroup 2 is invalid and will be ignored +80: [14:17:38] Explicit valence for atom # 2 O, 3, is greater than permitted +80: [14:17:38] Explicit valence for atom # 1 O, 3, is greater than permitted +80: [14:17:38] Explicit valence for atom # 1 C, 5, is greater than permitted +80: [14:17:38] sanitize [14:17:38] UNK: [14:17:38] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +80: [14:17:38] skipping block at line 7: 'BEGIN ATOM' 80: ATOM 1 CHLO CHL 0 0.000 0.000 0.000 1.00 0.00 CL 80: END 80: -81: Randomness seeded to: 3887494849 -81: =============================================================================== -81: All tests passed (95 assertions in 4 test cases) -81: - 58/236 Test #81: testPropertyLists ...................... Passed 0.08 sec -82: Randomness seeded to: 841149313 -82: =============================================================================== -82: All tests passed (100 assertions in 2 test cases) -82: -test 98 - Start 98: pyChemReactionEnumerations - -98: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py" -98: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap -98: Test timeout computed to be: 1500 -test 99 - Start 99: pyChemReactionSanitize - -99: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/testSanitize.py" -99: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap -99: Test timeout computed to be: 1500 -test 100 - Start 100: testChemTransforms - -100: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/testChemTransforms -100: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms -100: Test timeout computed to be: 1500 -60: Test -60: -60: RP-6306_3d.cxsmi -60: -60: Test -60: -60: Sotorasib_atrop1.cxsmi -60: -60: Test -60: -60: Sotorasib_atrop2.cxsmi -60: -60: Test -60: -60: Sotorasib_atrop3.cxsmi -60: -60: Test -60: -60: Sotorasib_atrop4.cxsmi -60: -60: Test -60: -60: Sotorasib_atrop5.cxsmi -60: -60: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: Test -60: -60: Sotorasib_atropBad1.cxsmi -60: -60: [17:55:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -60: [17:55:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -60: [17:55:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -60: [17:55:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -70: [17:55:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 -70: [17:55:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 -70: [17:55:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 -70: [17:55:19] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -70: [17:55:19] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -70: [17:55:19] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -70: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -72: [17:55:19] Finished: testMixIterAndRandom() -72: [17:55:19] ----------------------------------------- -72: -72: [17:55:19] ----------------------------------------- -72: build: -72: [17:55:19] Finished: testRemoveHs() -72: [17:55:19] ----------------------------------------- -72: -72: [17:55:19] ----------------------------------------- -72: [17:55:19] Finished: testGetItemText() -72: [17:55:19] ----------------------------------------- -72: -72: [17:55:19] ----------------------------------------- -46: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -46: [17:55:19] Explicit valence for atom # 0 Al, 6, is greater than permitted -46: [17:55:19] Explicit valence for atom # 0 Al, 6, is greater than permitted -46: [17:55:19] Explicit valence for atom # 1 Si, 6, is greater than permitted -46: [17:55:19] Explicit valence for atom # 1 Si, 6, is greater than permitted -46: [17:55:19] Explicit valence for atom # 0 P, 6, is greater than permitted -46: [17:55:19] Explicit valence for atom # 0 P, 6, is greater than permitted -46: [17:55:19] Explicit valence for atom # 0 P, 7, is greater than permitted -46: [17:55:19] Explicit valence for atom # 0 P, 7, is greater than permitted -46: [17:55:19] Explicit valence for atom # 1 As, 6, is greater than permitted -46: [17:55:19] Explicit valence for atom # 1 As, 6, is greater than permitted -46: [17:55:19] Explicit valence for atom # 1 As, 7, is greater than permitted -46: [17:55:19] Explicit valence for atom # 1 As, 7, is greater than permitted -46: [17:55:19] Explicit valence for atom # 0 Sb, 6, is greater than permitted -46: [17:55:19] Explicit valence for atom # 0 Sb, 6, is greater than permitted -46: [17:55:19] Explicit valence for atom # 0 Sb, 7, is greater than permitted -46: [17:55:19] Explicit valence for atom # 0 Sb, 7, is greater than permitted -46: [17:55:19] Explicit valence for atom # 1 Bi, 6, is greater than permitted -46: [17:55:19] Explicit valence for atom # 1 Bi, 6, is greater than permitted -46: [17:55:19] Explicit valence for atom # 1 Bi, 8, is greater than permitted -46: [17:55:19] Explicit valence for atom # 1 Bi, 8, is greater than permitted -46: =============================================================================== -46: All tests passed (4479 assertions in 107 test cases) -46: - 59/236 Test #25: pyAlignment ............................ Passed 2.74 sec -80: [17:55:19] +80: [14:17:38] 80: 80: **** 80: Pre-condition Violation @@ -20200,21 +19810,21 @@ 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::v2::FileParsers::SDMolSupplier::next() in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 3# 0x0000561A06AD43C4 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 4# 0x0000561A06A8FCAD in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 5# 0x0000561A06B18228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 6# 0x0000561A06B18D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 7# 0x0000561A06B191C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x0000561A06AEA8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000561A06AEAC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000561A06A5DC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x00007FF988233CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 3# 0x000055D8E676D3C4 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 4# 0x000055D8E6728CAD in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 5# 0x000055D8E67B1228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 6# 0x000055D8E67B1D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 7# 0x000055D8E67B21C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x000055D8E67838C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x000055D8E6783C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x000055D8E66F6C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x00007FBDC4233CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 13# 0x0000561A06A5DC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x000055D8E66F6C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [17:55:19] +80: [14:17:38] 80: 80: **** 80: Pre-condition Violation @@ -20226,23 +19836,64 @@ 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::v2::FileParsers::ForwardSDMolSupplier::next() in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 3# 0x0000561A06AD43C4 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 4# 0x0000561A06A8FE88 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 5# 0x0000561A06B18228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 6# 0x0000561A06B18D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 7# 0x0000561A06B191C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x0000561A06AEA8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000561A06AEAC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000561A06A5DC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x00007FF988233CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 3# 0x000055D8E676D3C4 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 4# 0x000055D8E6728E88 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 5# 0x000055D8E67B1228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 6# 0x000055D8E67B1D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 7# 0x000055D8E67B21C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x000055D8E67838C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x000055D8E6783C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x000055D8E66F6C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x00007FBDC4233CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 13# 0x0000561A06A5DC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x000055D8E66F6C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [17:55:19] +80: [14:17:38] 80: 80: **** +82: Randomness seeded to: 2820264323 +82: =============================================================================== +82: All tests passed (100 assertions in 2 test cases) +82: + 62/236 Test #82: XYZFileParserCatchTest ................. Passed 0.32 sec +test 97 + Start 97: pyChemReactions + +97: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py" +97: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap +97: Test timeout computed to be: 1500 +test 98 + Start 98: pyChemReactionEnumerations + +98: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py" +98: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap +98: Test timeout computed to be: 1500 +test 99 + Start 99: pyChemReactionSanitize + +99: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/testSanitize.py" +99: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap +99: Test timeout computed to be: 1500 +test 100 + Start 100: testChemTransforms + +100: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/testChemTransforms +100: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms +100: Test timeout computed to be: 1500 +test 101 + Start 101: chemTransformsTestCatch + +101: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms +101: Test timeout computed to be: 1500 +test 102 + Start 102: tautomerQueryTestCatch + +102: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/tautomerQueryTestCatch +102: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery +102: Test timeout computed to be: 1500 80: Pre-condition Violation 80: no stream 80: Violation occurred on line 409 in file ./Code/GraphMol/FileParsers/SmilesMolSupplier.cpp @@ -20252,21 +19903,21 @@ 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::v2::FileParsers::SmilesMolSupplier::next() in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 3# 0x0000561A06AD43C4 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 4# 0x0000561A06A902C1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 5# 0x0000561A06B18228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 6# 0x0000561A06B18D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 7# 0x0000561A06B191C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x0000561A06AEA8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000561A06AEAC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000561A06A5DC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x00007FF988233CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 3# 0x000055D8E676D3C4 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 4# 0x000055D8E67292C1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 5# 0x000055D8E67B1228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 6# 0x000055D8E67B1D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 7# 0x000055D8E67B21C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x000055D8E67838C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x000055D8E6783C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x000055D8E66F6C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x00007FBDC4233CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 13# 0x0000561A06A5DC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x000055D8E66F6C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [17:55:19] +80: [14:17:38] 80: 80: **** 80: Pre-condition Violation @@ -20278,21 +19929,21 @@ 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::v2::FileParsers::TDTMolSupplier::next() in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 3# 0x0000561A06AD43C4 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 4# 0x0000561A06A90646 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 5# 0x0000561A06B18228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 6# 0x0000561A06B18D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 7# 0x0000561A06B191C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x0000561A06AEA8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000561A06AEAC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000561A06A5DC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x00007FF988233CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 3# 0x000055D8E676D3C4 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 4# 0x000055D8E6729646 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 5# 0x000055D8E67B1228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 6# 0x000055D8E67B1D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 7# 0x000055D8E67B21C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x000055D8E67838C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x000055D8E6783C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x000055D8E66F6C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x00007FBDC4233CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 13# 0x0000561A06A5DC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x000055D8E66F6C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [17:55:19] +80: [14:17:38] 80: 80: **** 80: Pre-condition Violation @@ -20304,29 +19955,29 @@ 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::v2::FileParsers::MaeMolSupplier::next() in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 3# 0x0000561A06AD43C4 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 4# 0x0000561A06A908C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 5# 0x0000561A06B18228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 6# 0x0000561A06B18D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 7# 0x0000561A06B191C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x0000561A06AEA8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000561A06AEAC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000561A06A5DC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x00007FF988233CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 3# 0x000055D8E676D3C4 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 4# 0x000055D8E67298C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 5# 0x000055D8E67B1228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 6# 0x000055D8E67B1D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 7# 0x000055D8E67B21C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x000055D8E67838C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x000055D8E6783C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x000055D8E66F6C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x00007FBDC4233CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 13# 0x0000561A06A5DC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x000055D8E66F6C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [17:55:19] Found a SCD/SED line with missing/empty SDT specification at line 21 -80: [17:55:19] Found a SCD/SED line with missing/empty SDT specification at line 20 -80: [17:55:19] BEGIN SGROUP line not found on line 14 -80: [17:55:19] Unhandled CTAB feature: 'Unsupported SGroup type '' on line 18'. Molecule skipped. -80: [17:55:19] END SGROUP line not found on line 14 -80: [17:55:19] END SGROUP line not found on line 14 -80: [17:55:19] MRV_COORDINATE_BOND_TYPE SGroup with value 0 does not reference a query bond, ignoring. -80: [17:55:19] MRV_COORDINATE_BOND_TYPE SGroup with value 1 does not reference a query bond, ignoring. -80: [17:55:19] +80: [14:17:38] Found a SCD/SED line with missing/empty SDT specification at line 21 +80: [14:17:38] Found a SCD/SED line with missing/empty SDT specification at line 20 +80: [14:17:38] BEGIN SGROUP line not found on line 14 +80: [14:17:38] Unhandled CTAB feature: 'Unsupported SGroup type '' on line 18'. Molecule skipped. +80: [14:17:38] END SGROUP line not found on line 14 +80: [14:17:38] END SGROUP line not found on line 14 +80: [14:17:38] MRV_COORDINATE_BOND_TYPE SGroup with value 0 does not reference a query bond, ignoring. +80: [14:17:38] MRV_COORDINATE_BOND_TYPE SGroup with value 1 does not reference a query bond, ignoring. +80: [14:17:38] 80: 80: **** 80: Range Error @@ -20341,38 +19992,38 @@ 80: 3# RDKit::FileParserUtils::finishMolProcessing(RDKit::RWMol*, bool, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 4# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 5# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 6# 0x0000561A06AD3FDF in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 7# 0x0000561A06A95CC3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x0000561A06B18228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000561A06B18D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000561A06B191C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000561A06AEA8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000561A06AEAC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000561A06A5DC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x00007FF988233CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 6# 0x000055D8E676CFDF in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 7# 0x000055D8E672ECC3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x000055D8E67B1228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x000055D8E67B1D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x000055D8E67B21C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x000055D8E67838C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x000055D8E6783C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x000055D8E66F6C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x00007FBDC4233CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 15# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 16# 0x0000561A06A5DC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x000055D8E66F6C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [17:55:19] molecule does not contain a bond matching the MRV_COORDINATE_BOND_TYPE SGroup for bond 99, ignoring. -80: [17:55:19] Multiple ATTCHPT values for atom 2 on line 9 -80: [17:55:19] Found a SCD/SED line with missing/empty SDT specification at line 12 -80: [17:55:19] SMARTS Parse Error: syntax error while parsing: [#6;R -80: [17:55:19] SMARTS Parse Error: Failed parsing SMARTS '[#6;R' for input: '[#6;R' -80: [17:55:19] SMARTS for SMARTSQ '[#6;R' could not be parsed or has no atoms. Ignoring it. -80: [17:55:19] Skipping empty SMARTS value for SMARTSQ. -80: [17:55:19] unrecognized QUERYOP '>' for SMARTSQ. Query ignored. -80: [17:55:19] Found a SCD/SED line with missing/empty SDT specification at line 12 -80: [17:55:19] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -80: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -80: [17:55:19] WARNING: Skipping property bar because the value includes an illegal blank line -80: [17:55:19] WARNING: Skipping property baz because the value includes an illegal blank line -80: [17:55:19] WARNING: Skipping property bletch +80: [14:17:38] molecule does not contain a bond matching the MRV_COORDINATE_BOND_TYPE SGroup for bond 99, ignoring. +80: [14:17:38] Multiple ATTCHPT values for atom 2 on line 9 +80: [14:17:38] Found a SCD/SED line with missing/empty SDT specification at line 12 +80: [14:17:38] SMARTS Parse Error: syntax error while parsing: [#6;R +80: [14:17:38] SMARTS Parse Error: Failed parsing SMARTS '[#6;R' for input: '[#6;R' +80: [14:17:38] SMARTS for SMARTSQ '[#6;R' could not be parsed or has no atoms. Ignoring it. +80: [14:17:38] Skipping empty SMARTS value for SMARTSQ. +80: [14:17:38] unrecognized QUERYOP '>' for SMARTSQ. Query ignored. +80: [14:17:38] Found a SCD/SED line with missing/empty SDT specification at line 12 +80: [14:17:38] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +80: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +80: [14:17:38] WARNING: Skipping property bar because the value includes an illegal blank line +80: [14:17:38] WARNING: Skipping property baz because the value includes an illegal blank line +80: [14:17:38] WARNING: Skipping property bletch 80: nope because the name includes a newline -80: [17:55:19] WARNING: Skipping property bletch +80: [14:17:38] WARNING: Skipping property bletch 80: nope2 because the name includes a newline -80: [17:55:19] +80: [14:17:38] 80: 80: **** 80: Post-condition Violation @@ -20384,26 +20035,26 @@ 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 3# 0x00007FF988CC8531 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 4# 0x00007FF988CD3AC2 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# 0x00007FF988CD4FAD in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 3# 0x00007FBDC4CC8531 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 4# 0x00007FBDC4CD3AC2 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x00007FBDC4CD4FAD in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 9# 0x0000561A06A6735C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000561A06B18228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000561A06B18D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000561A06B191C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000561A06AEA8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000561A06AEAC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000561A06A5DC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x00007FF988233CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 9# 0x000055D8E670035C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x000055D8E67B1228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x000055D8E67B1D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x000055D8E67B21C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x000055D8E67838C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x000055D8E6783C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x000055D8E66F6C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x00007FBDC4233CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 18# 0x0000561A06A5DC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x000055D8E66F6C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [17:55:19] +80: [14:17:38] 80: 80: **** 80: Post-condition Violation @@ -20415,26 +20066,26 @@ 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 3# 0x00007FF988CC8531 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 4# 0x00007FF988CD3AC2 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# 0x00007FF988CD4FAD in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 3# 0x00007FBDC4CC8531 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 4# 0x00007FBDC4CD3AC2 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x00007FBDC4CD4FAD in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 9# 0x0000561A06A66A3A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000561A06B18228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000561A06B18D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000561A06B191C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000561A06AEA8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000561A06AEAC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000561A06A5DC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x00007FF988233CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 9# 0x000055D8E66FFA3A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x000055D8E67B1228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x000055D8E67B1D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x000055D8E67B21C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x000055D8E67838C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x000055D8E6783C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x000055D8E66F6C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x00007FBDC4233CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 18# 0x0000561A06A5DC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x000055D8E66F6C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [17:55:19] +80: [14:17:38] 80: 80: **** 80: Post-condition Violation @@ -20446,109 +20097,289 @@ 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 3# 0x00007FF988CC8531 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 4# 0x00007FF988CD1DFA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# 0x00007FF988CD217D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 3# 0x00007FBDC4CC8531 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 4# 0x00007FBDC4CD1DFA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x00007FBDC4CD217D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 6# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 9# 0x0000561A06A67304 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000561A06B18228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000561A06B18D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000561A06B191C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000561A06AEA8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000561A06AEAC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000561A06A5DC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x00007FF988233CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 9# 0x000055D8E6700304 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x000055D8E67B1228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x000055D8E67B1D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x000055D8E67B21C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x000055D8E67838C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x000055D8E6783C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x000055D8E66F6C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x00007FBDC4233CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 18# 0x0000561A06A5DC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x000055D8E66F6C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [17:55:19] +80: [14:17:38] 80: 80: **** - 60/236 Test #82: XYZFileParserCatchTest ................. Passed 0.09 sec -69: [17:55:19] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) -69: [17:55:19] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) -69: [17:55:19] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +80: Post-condition Violation +80: Element 'QQQ' not found +80: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h +80: Failed Expression: anum > -1 +80: ---------- +80: Stacktrace: +80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +80: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 3# 0x00007FBDC4CC8531 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 4# 0x00007FBDC4CD1DFA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x00007FBDC4CD217D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 6# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 9# 0x000055D8E66FFFA2 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x000055D8E67B1228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x000055D8E67B1D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x000055D8E67B21C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x000055D8E67838C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x000055D8E6783C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x000055D8E66F6C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x00007FBDC4233CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +80: 18# 0x000055D8E66F6C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: ---------- +80: **** +80: +80: [14:17:38] atom 3 has a negative isotope value. line: 15 +58: --C1CCC2(CC1)CCCCC2CCC1CCCC1 +58: smi: ClC1CCCCC1 +58: smi: ClC1CCCCC1 +58: smi: ClC1CCCCC1Br +58: smi: c1ccccc1 +58: smi: c1ccncc1 +58: smi: c1cc[nH]c1 +58: smi: c1cc[nH]c1 +58: smi: c1cc[pH]c1 +58: [14:17:38] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +58: [14:17:38] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +58: CbC(aC)aC +58: CaC(bC)aC +58: CbC(bC)aC +58: O.C +58: 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 +58: [14:17:38] SMILES Parse Error: syntax error while parsing: c%()ccccc%() +58: [14:17:38] SMILES Parse Error: check for mistakes around position 4: +58: [14:17:38] c%()ccccc%() +58: [14:17:38] ~~~^ +58: [14:17:38] SMILES Parse Error: Failed parsing SMILES 'c%()ccccc%()' for input: 'c%()ccccc%()' +58: [14:17:38] SMILES Parse Error: syntax error while parsing: c%(100000)ccccc%(100000) +58: [14:17:38] SMILES Parse Error: check for mistakes around position 9: +58: [14:17:38] c%(100000)ccccc%(100000) +58: [14:17:38] ~~~~~~~~^ +58: [14:17:38] SMILES Parse Error: Failed parsing SMILES 'c%(100000)ccccc%(100000)' for input: 'c%(100000)ccccc%(100000)' +58: [14:17:38] SMILES Parse Error: duplicated ring closure 1 bonds atom 2 to itself for input: 'C1CC111' +58: [14:17:38] SMILES Parse Error: ring closure 1 duplicates bond between atom 0 and atom 1 for input: 'C1C1' +58: [14:17:38] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +58: [14:17:38] SMILES Parse Error: check for mistakes around position 14: +58: [14:17:38] COc(c1)cccc1C# +58: [14:17:38] ~~~~~~~~~~~~~^ +58: [14:17:38] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +58: [14:17:38] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +58: [14:17:38] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +58: [14:17:38] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +58: [14:17:38] SMILES Parse Error: check for mistakes around position 14: +58: [14:17:38] COc(c1)cccc1C# +58: [14:17:38] ~~~~~~~~~~~~~^ +58: [14:17:38] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +58: [14:17:38] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +58: [14:17:38] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +58: [14:17:38] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +58: [14:17:38] SMILES Parse Error: check for mistakes around position 14: +58: [14:17:38] COc(c1)cccc1C# +58: [14:17:38] ~~~~~~~~~~~~~^ +58: [14:17:38] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +58: [14:17:38] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +58: [14:17:38] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +58: C=c1s/c2n(c1=O)CCCCCCC\N=2 +58: C1=C\C/C=C2C3=C\C/C=C\C=C/C/3C\2\C=C/1 +58: [14:17:38] SMILES Parse Error: extra close parentheses while parsing: C) +58: [14:17:38] SMILES Parse Error: check for mistakes around position 2: +58: [14:17:38] C) +58: [14:17:38] ~^ +58: [14:17:38] SMILES Parse Error: Failed parsing SMILES 'C)' for input: 'C)' +70: [14:17:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [14:17:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [14:17:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [14:17:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [14:17:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [14:17:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [14:17:38] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +70: [14:17:38] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +70: [14:17:38] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +70: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [14:17:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +70: [14:17:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +70: [14:17:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +70: [14:17:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [14:17:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [14:17:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [14:17:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [14:17:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [14:17:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [14:17:38] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +70: [14:17:38] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +70: [14:17:38] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +70: [14:17:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [14:17:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [14:17:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +70: [14:17:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [14:17:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [14:17:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +70: [14:17:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [14:17:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [14:17:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +70: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +68: Test +68: +68: NewChiralTest.sdf +68: +68: Test +68: +68: NewChiralTest.sdf +68: +68: Test +68: +68: NewChiralTestNoChiral.sdf +68: +68: Test +68: +68: NewChiralTestNoChiral.sdf +68: +68: Test +68: +68: NewChiralTestAllChiral.sdf +68: +68: Test +68: +68: NewChiralTestAllChiral.sdf +68: +68: Test +68: +68: vendor839.sdf +68: +68: Test +68: +68: ProblemShort.mol +68: +68: [14:17:38] For a MultipleSgroup expansion, the matching orphaned bond was not found +68: The multiple sgroup will be ignored +86: Randomness seeded to: 1859332804 +86: [14:17:38] Ignoring invalid chirality label: '12_R_1_3_4_5' +86: [14:17:38] Ignoring invalid chirality label: '12_ANR_1_3_4_15' +86: [14:17:38] Ignoring invalid chirality label: '2_S_1_3_4' +86: [14:17:38] Ignoring invalid chirality label: '2_ANS_1_3_4_5_2' +86: =============================================================================== +86: All tests passed (24 assertions in 6 test cases) +86: +69: [14:17:38] bond with order 0 found on line 7. This is not part of the MDL specification. +69: [14:17:38] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) +69: [14:17:38] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) +69: [14:17:38] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 69: generating smiles 69: 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 69: converting back 69: check isomorphism -85: Randomness seeded to: 3734071683 +85: Randomness seeded to: 4229275608 85: =============================================================================== 85: All tests passed (8 assertions in 1 test case) 85: - 61/236 Test #85: connectTheDotsTest ..................... Passed 0.08 sec -2: .... -2: ---------------------------------------------------------------------- -2: Ran 4 tests in 0.030s -2: -2: OK -84: Randomness seeded to: 1241516006 -84: [17:55:19] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -84: [17:55:19] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -84: [17:55:19] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -84: [17:55:19] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +83: Randomness seeded to: 3396048897 +83: [14:17:38] Invalid or missing fragment id from CDXML fragment, assigning new one... +83: [14:17:38] Explicit valence for atom # 3 N, 4, is greater than permitted +83: [14:17:38] CDXMLParser: failed sanitizing skipping fragment 32 +83: [14:17:38] Bad bond in CDXML skipping fragment 58... +83: [14:17:38] Invalid or missing fragment id from CDXML fragment, assigning new one... +83: [14:17:38] Bad bond in CDXML skipping fragment 58... +83: [14:17:38] WARNING: not removing hydrogen atom without neighbors +83: [14:17:38] WARNING: not removing hydrogen atom without neighbors +83: [14:17:38] WARNING: not removing hydrogen atom without neighbors +83: [14:17:38] WARNING: not removing hydrogen atom without neighbors +83: [14:17:38] WARNING: not removing hydrogen atom without neighbors +83: [14:17:38] WARNING: not removing hydrogen atom without neighbors +83: [14:17:38] WARNING: not removing hydrogen atom without neighbors +83: [14:17:38] WARNING: not removing hydrogen atom without neighbors +83: [14:17:38] WARNING: not removing hydrogen atom without neighbors +83: [14:17:38] WARNING: not removing hydrogen atom without neighbors +83: [14:17:38] CDXMLParser: Schema 80180 step 80181 ReactionStepAgents reaction fragment 64603 not found in document. +83: [14:17:38] Incomplete atom labelling, cannot make bond +83: [14:17:38] Incomplete atom labelling, cannot make bond +83: [14:17:38] Incomplete atom labelling, cannot make bond +83: [14:17:38] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas +83: [14:17:38] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas +83: [14:17:38] Failed to parse XML fragment 5 node: b attribute: Order: slartibartfast +83: [14:17:38] Failed to parse XML fragment 5 node: b attribute: Order: 5 +83: [14:17:38] Invalid or missing fragment id from CDXML fragment, assigning new one... +83: =============================================================================== +83: All tests passed (263 assertions in 7 test cases) +83: +84: Randomness seeded to: 3273460125 +84: [14:17:38] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +84: [14:17:38] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +84: [14:17:38] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +84: [14:17:38] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. 84: =============================================================================== 84: All tests passed (142 assertions in 6 test cases) 84: - 62/236 Test #84: molfileStereoCatchTest ................. Passed 0.08 sec -21: .................... -21: ---------------------------------------------------------------------- -21: Ran 20 tests in 0.087s -21: -21: OK -21: Testing Geometry wrapper -73: [17:55:19] Finished: testMae() -73: [17:55:19] ----------------------------------------- +73: [14:17:38] Finished: testMae() +73: [14:17:38] ----------------------------------------- 73: -73: [17:55:19] +73: [14:17:38] 73: ----------------------------------------- -73: [17:55:19] Finished: testTdt() -73: [17:55:19] ----------------------------------------- +73: [14:17:38] Finished: testTdt() +73: [14:17:38] ----------------------------------------- 73: - 63/236 Test #73: testGeneralFileReader .................. Passed 0.25 sec -83: Randomness seeded to: 533316399 -83: [17:55:19] Invalid or missing fragment id from CDXML fragment, assigning new one... -83: [17:55:19] Explicit valence for atom # 3 N, 4, is greater than permitted -83: [17:55:19] CDXMLParser: failed sanitizing skipping fragment 32 -83: [17:55:19] Bad bond in CDXML skipping fragment 58... -83: [17:55:19] Invalid or missing fragment id from CDXML fragment, assigning new one... -83: [17:55:19] Bad bond in CDXML skipping fragment 58... -83: [17:55:19] WARNING: not removing hydrogen atom without neighbors -83: [17:55:19] WARNING: not removing hydrogen atom without neighbors -83: [17:55:19] WARNING: not removing hydrogen atom without neighbors -83: [17:55:19] WARNING: not removing hydrogen atom without neighbors -83: [17:55:19] WARNING: not removing hydrogen atom without neighbors -35: [17:55:19] Maximum BFS search size exceeded. -35: This is likely due to a highly symmetric fused ring system. -35: F/C=C/Cl -35: [H]/C(F)=C(/[H])Cl -35: F/C=C/Cl -35: F/C=C/Cl -35: C/C(F)=C(/C)Cl -30: ...[17:55:19] Molecule does not have explicit Hs. Consider calling AddHs() -86: Randomness seeded to: 3687650107 -86: [17:55:19] Ignoring invalid chirality label: '12_R_1_3_4_5' -86: [17:55:19] Ignoring invalid chirality label: '12_ANR_1_3_4_15' -86: [17:55:19] Ignoring invalid chirality label: '2_S_1_3_4' -86: [17:55:19] Ignoring invalid chirality label: '2_ANS_1_3_4_5_2' -86: =============================================================================== -86: All tests passed (24 assertions in 6 test cases) -86: - 64/236 Test #86: v2MolSuppliers ......................... Passed 0.06 sec -87: Randomness seeded to: 2131754076 +72: [14:17:38] Finished: testMolSup() +72: [14:17:38] ----------------------------------------- +72: +72: [14:17:38] ----------------------------------------- +72: [14:17:38] Finished: testRandMolSup() +72: [14:17:38] ----------------------------------------- +72: +72: [14:17:38] ----------------------------------------- +72: [14:17:38] Finished: testSmilesSup() +72: [14:17:38] ----------------------------------------- +72: +72: [14:17:38] ----------------------------------------- +72: [14:17:38] ------------------------------------------------------ +72: [14:17:38] SMILES Parse Error: syntax error while parsing: fail +72: [14:17:38] SMILES Parse Error: check for mistakes around position 1: +72: [14:17:38] fail +72: [14:17:38] ^ +72: [14:17:38] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' +72: [14:17:38] ERROR: Smiles parse error on line 3 +72: [14:17:38] ERROR: Cannot create molecule from : 'fail' +72: [14:17:38] ------------------------------------------------------ +72: [14:17:38] ------------------------------------------------------ +72: [14:17:38] >>> This may result in an infinite loop. It should finish almost immediately: +72: [14:17:38] <<< done. +72: [14:17:38] Finished: testSmilesSupFromText() +72: [14:17:38] ----------------------------------------- +72: +72: [14:17:38] ----------------------------------------- +72: [14:17:38] Finished: testSmilesWriter() +72: [14:17:38] ----------------------------------------- +72: +72: [14:17:38] ----------------------------------------- +40: [14:17:38] sorting (hanoi sort) vectors +87: Randomness seeded to: 204011099 87: =============================================================================== 87: All tests passed (6 assertions in 1 test case) 87: - 65/236 Test #87: v2FileParsersCatchTest ................. Passed 0.06 sec -88: Randomness seeded to: 1853381304 +88: Randomness seeded to: 3464941865 88: =============================================================================== 88: All tests passed (26 assertions in 2 test cases) 88: - 66/236 Test #88: atropisomersCatch ...................... Passed 0.06 sec 90: ----------------- Test 1 90: Done 90: @@ -20573,25 +20404,188 @@ 90: ----------------- Testing serial numbers on recursive queries 90: Done 90: -90: [17:55:19] ------------------------------------- -90: [17:55:19] Test multithreading +90: [14:17:38] ------------------------------------- +90: [14:17:38] Test multithreading 90: reading molecules -94: [17:55:19] ------------------------------------- -94: [17:55:19] Test Reaction StructuralFingerprint -94: [17:55:19] ------------------------------------- -94: [17:55:19] Test Reaction DifferenceFingerprint -test 101 - Start 101: chemTransformsTestCatch - -101: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms -101: Test timeout computed to be: 1500 -test 102 - Start 102: tautomerQueryTestCatch - -102: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/tautomerQueryTestCatch -102: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery -102: Test timeout computed to be: 1500 +90: hits: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 +90: processing +90: launch :0 +90: launch :1 +90: launch :2 +90: launch :3 +93: smi: O=C1CNC(=O)CN1 +93: 1: O=C1CNC(=O)CN1 +93: 2: COOC +93: [14:17:38] SMARTS Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] +93: [14:17:38] 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]' +93: O=C1CNC(=O)CN1 +93: [14:17:38] product atom-mapping number 1 found multiple times. +93: [14:17:38] mapped atoms in the reactants were not mapped in the products. +93: unmapped numbers are: 4 +93: [14:17:38] atom 0 in product 0 has multiple charge specifications. +93: mass: 15.0001 +93: Oc1ccccn1 +93: Oc1ccc[nH]1 +93: [14:17:38] SMARTS Parse Error: syntax error while parsing: ([C:1](=O)O.[C:2] +93: [14:17:38] SMARTS Parse Error: Failed parsing SMARTS '([C:1](=O)O.[C:2]' for input: '([C:1](=O)O.[C:2]' +93: [14:17:38] SMARTS Parse Error: syntax error while parsing: ([C:2] +93: [14:17:38] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' +93: [14:17:38] SMARTS Parse Error: syntax error while parsing: [C:1](=O)O).[C:2] +93: [14:17:38] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=O)O).[C:2]' for input: '[C:1](=O)O).[C:2]' +93: [14:17:38] SMARTS Parse Error: syntax error while parsing: [C:2]) +93: [14:17:38] SMARTS Parse Error: Failed parsing SMARTS '[C:2])' for input: '[C:2])' +93: [14:17:38] SMILES Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] +93: [14:17:38] SMILES Parse Error: check for mistakes around position 2: +93: [14:17:38] [Q:1][C:2][C:3](=[O:4])[O:5] +93: [14:17:38] ~^ +93: [14:17:38] 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]' +93: [14:17:38] reactant 2 has no mapped atoms. +93: [14:17:38] >> Atoms within one molecule have different RXN roles. +93: [14:17:38] >> Fragment 0 not included in the reaction, atoms do not have a correct RXN role. +93: [14:17:38] SMARTS Parse Error: syntax error while parsing: ([C:1][C:2] +93: [14:17:38] SMARTS Parse Error: Failed parsing SMARTS '([C:1][C:2]' for input: '([C:1][C:2]' +93: [14:17:38] SMARTS Parse Error: syntax error while parsing: ([C:2] +93: [14:17:38] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' +93: [14:17:38] SMARTS Parse Error: syntax error while parsing: [C:1][C:2]) +93: [14:17:38] SMARTS Parse Error: Failed parsing SMARTS '[C:1][C:2])' for input: '[C:1][C:2])' +93: [14:17:38] SMARTS Parse Error: syntax error while parsing: [C:1]).[C:2] +93: [14:17:38] SMARTS Parse Error: Failed parsing SMARTS '[C:1]).[C:2]' for input: '[C:1]).[C:2]' +93: [14:17:38] reactant 0 has no mapped atoms. +93: [14:17:38] reactant 1 has no mapped atoms. +93: [14:17:38] reactant 3 has no mapped atoms. +93: [14:17:38] product atom-mapping number 2 found multiple times. +93: [14:17:38] product atom-mapping number 3 found multiple times. +93: [14:17:38] product atom-mapping number 4 found multiple times. +93: [14:17:38] product atom-mapping number 5 found multiple times. +93: [14:17:38] product atom-mapping number 6 found multiple times. +93: [14:17:38] product atom-mapping number 7 found multiple times. +93: [14:17:38] product atom-mapping number 8 found multiple times. +93: [14:17:38] product atom-mapping number 12 found multiple times. +93: [14:17:38] product atom-mapping number 9 found multiple times. +93: [14:17:38] product atom-mapping number 10 found multiple times. +93: [14:17:38] product atom-mapping number 11 found multiple times. +93: [14:17:38] reactant 0 has no mapped atoms. +93: [14:17:38] reactant 1 has no mapped atoms. +93: [14:17:38] reactant 3 has no mapped atoms. +93: [14:17:38] reactant atom-mapping number 19 found multiple times. +93: [14:17:38] reactant atom-mapping number 25 found multiple times. +93: [14:17:38] reactant atom-mapping number 20 found multiple times. +93: [14:17:38] reactant atom-mapping number 21 found multiple times. +93: [14:17:38] reactant atom-mapping number 22 found multiple times. +93: [14:17:38] reactant atom-mapping number 23 found multiple times. +93: [14:17:38] reactant atom-mapping number 24 found multiple times. +93: [14:17:38] product atom-mapping number 1 found multiple times. +93: [14:17:38] product atom-mapping number 1 found multiple times. +93: [14:17:38] product atom-mapping number 1 found multiple times. +93: [14:17:38] product atom-mapping number 1 found multiple times. +93: [14:17:38] product atom-mapping number 2 found multiple times. +93: [14:17:38] product atom-mapping number 1 found multiple times. +93: [14:17:38] product atom-mapping number 2 found multiple times. +93: [14:17:38] product atom-mapping number 1 found multiple times. +93: [14:17:38] product atom-mapping number 2 found multiple times. +93: [14:17:38] product atom-mapping number 1 found multiple times. +93: [14:17:38] product atom-mapping number 2 found multiple times. +93: [14:17:38] product atom-mapping number 1 found multiple times. +93: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br +93: [14:17:38] product atom-mapping number 2 found multiple times. +93: [14:17:38] product atom-mapping number 1 found multiple times. +93: [14:17:38] product atom-mapping number 2 found multiple times. +93: [14:17:38] product atom-mapping number 1 found multiple times. +93: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br +93: [14:17:38] product atom-mapping number 5 found multiple times. +93: [14:17:38] product atom-mapping number 2 found multiple times. +93: [14:17:38] product atom-mapping number 3 found multiple times. +93: [14:17:38] product atom-mapping number 1 found multiple times. +93: [14:17:38] product atom-mapping number 4 found multiple times. +93: [14:17:38] product atom-mapping number 5 found multiple times. +93: [14:17:38] product atom-mapping number 2 found multiple times. +93: [14:17:38] product atom-mapping number 3 found multiple times. +93: [14:17:38] product atom-mapping number 1 found multiple times. +93: [14:17:38] product atom-mapping number 4 found multiple times. +93: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br +93: [14:17:38] product atom-mapping number 5 found multiple times. +93: [14:17:38] product atom-mapping number 2 found multiple times. +93: [14:17:38] product atom-mapping number 3 found multiple times. +93: [14:17:38] product atom-mapping number 1 found multiple times. +93: [14:17:38] product atom-mapping number 4 found multiple times. +93: [14:17:38] product atom-mapping number 5 found multiple times. +93: [14:17:38] product atom-mapping number 2 found multiple times. +93: [14:17:38] product atom-mapping number 3 found multiple times. +93: [14:17:38] product atom-mapping number 1 found multiple times. +93: [14:17:38] product atom-mapping number 4 found multiple times. +93: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br +93: [14:17:38] product atom-mapping number 2 found multiple times. +93: [14:17:38] product atom-mapping number 3 found multiple times. +93: [14:17:38] product atom-mapping number 1 found multiple times. +93: [14:17:38] product atom-mapping number 4 found multiple times. +93: [14:17:38] product atom-mapping number 2 found multiple times. +93: [14:17:38] product atom-mapping number 3 found multiple times. +93: [14:17:38] product atom-mapping number 1 found multiple times. +93: [14:17:38] product atom-mapping number 4 found multiple times. +93: F[C@@](Cl)(Br)O[C@](F)(Cl)Br +93: [14:17:38] product atom-mapping number 2 found multiple times. +93: [14:17:38] product atom-mapping number 3 found multiple times. +93: [14:17:38] product atom-mapping number 1 found multiple times. +93: [14:17:38] product atom-mapping number 4 found multiple times. +93: [14:17:38] product atom-mapping number 2 found multiple times. +93: [14:17:38] product atom-mapping number 3 found multiple times. +93: [14:17:38] product atom-mapping number 1 found multiple times. +93: [14:17:38] product atom-mapping number 4 found multiple times. +93: F[C@](Cl)(Br)O[C@](F)(Cl)Br +93: [14:17:38] product atom-mapping number 4 found multiple times. +93: [14:17:38] product atom-mapping number 3 found multiple times. +93: [14:17:38] product atom-mapping number 2 found multiple times. +93: [14:17:38] product atom-mapping number 1 found multiple times. +93: [14:17:38] product atom-mapping number 4 found multiple times. +93: [14:17:38] product atom-mapping number 3 found multiple times. +93: [14:17:38] product atom-mapping number 2 found multiple times. +93: [14:17:38] product atom-mapping number 1 found multiple times. +93: [14:17:38] product atom-mapping number 4 found multiple times. +93: [14:17:38] product atom-mapping number 3 found multiple times. +93: [14:17:38] product atom-mapping number 2 found multiple times. +93: [14:17:38] product atom-mapping number 1 found multiple times. +93: [14:17:38] product atom-mapping number 4 found multiple times. +93: [14:17:38] product atom-mapping number 3 found multiple times. +93: [14:17:38] product atom-mapping number 2 found multiple times. +93: [14:17:38] product atom-mapping number 1 found multiple times. +93: [14:17:38] product atom-mapping number 3 found multiple times. +93: [14:17:38] product atom-mapping number 2 found multiple times. +93: [14:17:38] product atom-mapping number 1 found multiple times. +93: [14:17:38] mapped atoms in the reactants were not mapped in the products. +93: unmapped numbers are: 4 +93: [14:17:38] product atom-mapping number 3 found multiple times. +93: [14:17:38] product atom-mapping number 2 found multiple times. +93: [14:17:38] product atom-mapping number 1 found multiple times. +93: [14:17:38] mapped atoms in the reactants were not mapped in the products. +93: unmapped numbers are: 4 +93: [14:17:38] product atom-mapping number 6 not found in reactants. +93: [14:17:38] product atom-mapping number 7 not found in reactants. +93: [14:17:38] product atom-mapping number 8 not found in reactants. +93: [14:17:38] product atom-mapping number 7 not found in reactants. +93: [14:17:38] product atom-mapping number 8 not found in reactants. +93: [14:17:38] product atom-mapping number 9 not found in reactants. +93: [14:17:38] product atom-mapping number 10 not found in reactants. +93: [14:17:38] mapped atoms in the reactants were not mapped in the products. +93: unmapped numbers are: 6 +93: [14:17:38] product atom-mapping number 7 not found in reactants. +93: [14:17:38] product atom-mapping number 8 not found in reactants. +93: [14:17:38] product atom-mapping number 9 not found in reactants. +93: [14:17:38] product atom-mapping number 10 not found in reactants. +93: [14:17:38] mapped atoms in the reactants were not mapped in the products. +93: unmapped numbers are: 6 +93: 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] +93: 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] +94: [14:17:38] ------------------------------------- +94: [14:17:38] Test Reaction StructuralFingerprint +94: [14:17:38] ------------------------------------- +94: [14:17:38] Test Reaction DifferenceFingerprint + 63/236 Test #73: testGeneralFileReader .................. Passed 0.60 sec + 64/236 Test #84: molfileStereoCatchTest ................. Passed 0.40 sec + 65/236 Test #85: connectTheDotsTest ..................... Passed 0.38 sec + 66/236 Test #86: v2MolSuppliers ......................... Passed 0.36 sec + 67/236 Test #87: v2FileParsersCatchTest ................. Passed 0.33 sec + 68/236 Test #88: atropisomersCatch ...................... Passed 0.32 sec + 69/236 Test #94: testReactionFingerprints ............... Passed 0.24 sec test 103 Start 103: pyTautomerQuery @@ -20628,135 +20622,14 @@ 108: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/Wrap/rough_test.py" 108: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap 108: Test timeout computed to be: 1500 -60: [17:55:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -60: Test -60: -60: Sotorasib_atropBad2.cxsmi -60: -60: [17:55:19] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -60: [17:55:19] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -60: [17:55:19] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -60: [17:55:19] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -60: [17:55:19] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -70: [17:55:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -70: [17:55:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -70: [17:55:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -70: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [17:55:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -70: [17:55:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -70: [17:55:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -72: [17:55:19] Finished: testForwardSDSupplier() -72: [17:55:19] ----------------------------------------- -72: -72: [17:55:19] ----------------------------------------- -72: [17:55:19] Finished: testMissingCRSDSupplier() -72: [17:55:19] ----------------------------------------- -72: -72: [17:55:19] ----------------------------------------- -72: [17:55:19] Finished: testIssue3482695() -72: [17:55:19] ----------------------------------------- -72: -72: [17:55:19] ----------------------------------------- -72: [17:55:19] ERROR: Cannot convert 'foo' to unsigned int on line 557 -72: [17:55:19] ERROR: moving to the beginning of the next molecule -72: [17:55:19] Finished: testIssue3525673() -72: [17:55:19] ----------------------------------------- -72: -72: [17:55:19] ----------------------------------------- -72: [17:55:19] Finished: testBlankLinesInProps() -72: [17:55:19] ----------------------------------------- -72: -72: [17:55:19] ----------------------------------------- -72: [17:55:19] Finished: testSkipLines() -72: [17:55:19] ----------------------------------------- -72: -72: [17:55:19] ----------------------------------------- -72: [17:55:19] Finished: testGitHub23() -72: [17:55:19] ----------------------------------------- -72: -72: [17:55:19] ----------------------------------------- -72: [17:55:19] Finished: testGitHub88() -72: [17:55:19] ----------------------------------------- -72: -72: [17:55:19] ----------------------------------------- -72: [17:55:19] Finished: testGitHub2285() -72: [17:55:19] ----------------------------------------- -72: -72: [17:55:19] ----------------------------------------- -72: [17:55:19] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -72: [17:55:19] ERROR: Smiles parse error on line 1 -72: [17:55:19] ERROR: Cannot create molecule from : 'c1ccccc' -72: [17:55:19] SMILES Parse Error: extra open parentheses while parsing: C(C -72: [17:55:19] SMILES Parse Error: check for mistakes around position 2: -72: [17:55:19] C(C -72: [17:55:19] ~^ -72: [17:55:19] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' -72: [17:55:19] ERROR: Smiles parse error on line 3 -72: [17:55:19] ERROR: Cannot create molecule from : 'C(C' -72: [17:55:19] Explicit valence for atom # 1 C, 5, is greater than permitted -72: [17:55:19] ERROR: Could not sanitize molecule on line 5 -72: [17:55:19] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted -72: [17:55:19] Explicit valence for atom # 1 F, 2, is greater than permitted -72: [17:55:19] ERROR: Could not sanitize molecule ending on line 21 -72: [17:55:19] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -72: [17:55:19] Explicit valence for atom # 1 F, 2, is greater than permitted -72: [17:55:19] ERROR: Could not sanitize molecule ending on line 21 -72: [17:55:19] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -72: [17:55:19] Explicit valence for atom # 1 F, 2, is greater than permitted -72: [17:55:19] ERROR: Could not sanitize molecule ending on line 21 -72: [17:55:19] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -72: [17:55:19] ERROR: Atom line too short: ' -9.6' on line 28 -72: [17:55:19] ERROR: moving to the beginning of the next molecule -72: [17:55:19] Explicit valence for atom # 1 F, 2, is greater than permitted -72: [17:55:19] ERROR: Could not sanitize molecule ending on line 21 -72: [17:55:19] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -72: [17:55:19] ERROR: Atom line too short: ' -9.6' on line 28 -72: [17:55:19] ERROR: moving to the beginning of the next molecule -72: [17:55:19] Finished: testGitHub2479() -72: [17:55:19] ----------------------------------------- -72: -72: [17:55:19] ----------------------------------------- -72: [17:55:19] Ignoring invalid chirality label: '7_S_8_9_6_10' -72: [17:55:19] Finished: testGitHub2881() -72: [17:55:19] ----------------------------------------- -72: -72: [17:55:19] ----------------------------------------- -72: [17:55:19] Finished: testGitHub3517() -72: [17:55:19] ----------------------------------------- -72: -80: Post-condition Violation -80: Element 'QQQ' not found -80: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h -80: Failed Expression: anum > -1 -80: ---------- -80: Stacktrace: -80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -80: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 3# 0x00007FF988CC8531 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 4# 0x00007FF988CD1DFA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# 0x00007FF988CD217D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 6# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 9# 0x0000561A06A66FA2 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000561A06B18228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000561A06B18D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000561A06B191C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000561A06AEA8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000561A06AEAC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000561A06A5DC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x00007FF988233CA8 in /lib/x86_64-linux-gnu/libc.so.6 -80: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 18# 0x0000561A06A5DC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: ---------- -80: **** -80: -80: [17:55:19] atom 3 has a negative isotope value. line: 15 -80: [17:55:19] Ignoring invalid chirality label: '2_bad_chirality' -80: [17:55:19] +test 109 + Start 109: testFragCatalog + +109: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog +109: Test timeout computed to be: 1500 +80: [14:17:38] Ignoring invalid chirality label: '2_bad_chirality' +80: [14:17:38] 80: 80: **** 80: Pre-condition Violation @@ -20769,239 +20642,117 @@ 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::v2::FileParsers::MaeMolSupplier::init() in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 3# RDKit::v2::FileParsers::MaeMolSupplier::reset() in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 4# 0x0000561A06AA97A5 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 5# 0x0000561A06B18228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 6# 0x0000561A06B18D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 7# 0x0000561A06B191C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x0000561A06AEA8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000561A06AEAC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000561A06A5DC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x00007FF988233CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 4# 0x000055D8E67427A5 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 5# 0x000055D8E67B1228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 6# 0x000055D8E67B1D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 7# 0x000055D8E67B21C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x000055D8E67838C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x000055D8E6783C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x000055D8E66F6C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x00007FBDC4233CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 13# 0x0000561A06A5DC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x000055D8E66F6C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -83: [17:55:19] WARNING: not removing hydrogen atom without neighbors -83: [17:55:19] WARNING: not removing hydrogen atom without neighbors -83: [17:55:19] WARNING: not removing hydrogen atom without neighbors -83: [17:55:19] WARNING: not removing hydrogen atom without neighbors -83: [17:55:19] WARNING: not removing hydrogen atom without neighbors -83: [17:55:19] CDXMLParser: Schema 80180 step 80181 ReactionStepAgents reaction fragment 64603 not found in document. -83: [17:55:19] Incomplete atom labelling, cannot make bond -83: [17:55:19] Incomplete atom labelling, cannot make bond -93: smi: O=C1CNC(=O)CN1 -93: 1: O=C1CNC(=O)CN1 -93: 2: COOC -93: [17:55:19] SMARTS Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] -93: [17:55:19] 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]' -93: O=C1CNC(=O)CN1 -93: [17:55:19] product atom-mapping number 1 found multiple times. -93: [17:55:19] mapped atoms in the reactants were not mapped in the products. -93: unmapped numbers are: 4 -93: [17:55:19] atom 0 in product 0 has multiple charge specifications. -93: mass: 15.0001 -93: Oc1ccccn1 -93: Oc1ccc[nH]1 -93: [17:55:19] SMARTS Parse Error: syntax error while parsing: ([C:1](=O)O.[C:2] -93: [17:55:19] SMARTS Parse Error: Failed parsing SMARTS '([C:1](=O)O.[C:2]' for input: '([C:1](=O)O.[C:2]' -93: [17:55:19] SMARTS Parse Error: syntax error while parsing: ([C:2] -93: [17:55:19] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' -93: [17:55:19] SMARTS Parse Error: syntax error while parsing: [C:1](=O)O).[C:2] -93: [17:55:19] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=O)O).[C:2]' for input: '[C:1](=O)O).[C:2]' -93: [17:55:19] SMARTS Parse Error: syntax error while parsing: [C:2]) -93: [17:55:19] SMARTS Parse Error: Failed parsing SMARTS '[C:2])' for input: '[C:2])' -93: [17:55:19] SMILES Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] -93: [17:55:19] SMILES Parse Error: check for mistakes around position 2: -93: [17:55:19] [Q:1][C:2][C:3](=[O:4])[O:5] -93: [17:55:19] ~^ -93: [17:55:19] 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]' -93: [17:55:19] reactant 2 has no mapped atoms. -93: [17:55:19] >> Atoms within one molecule have different RXN roles. -93: [17:55:19] >> Fragment 0 not included in the reaction, atoms do not have a correct RXN role. -93: [17:55:19] SMARTS Parse Error: syntax error while parsing: ([C:1][C:2] -93: [17:55:19] SMARTS Parse Error: Failed parsing SMARTS '([C:1][C:2]' for input: '([C:1][C:2]' -93: [17:55:19] SMARTS Parse Error: syntax error while parsing: ([C:2] -93: [17:55:19] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' -93: [17:55:19] SMARTS Parse Error: syntax error while parsing: [C:1][C:2]) -93: [17:55:19] SMARTS Parse Error: Failed parsing SMARTS '[C:1][C:2])' for input: '[C:1][C:2])' -93: [17:55:19] SMARTS Parse Error: syntax error while parsing: [C:1]).[C:2] -93: [17:55:19] SMARTS Parse Error: Failed parsing SMARTS '[C:1]).[C:2]' for input: '[C:1]).[C:2]' -93: [17:55:19] reactant 0 has no mapped atoms. -93: [17:55:19] reactant 1 has no mapped atoms. -93: [17:55:19] reactant 3 has no mapped atoms. -93: [17:55:19] product atom-mapping number 2 found multiple times. -93: [17:55:19] product atom-mapping number 3 found multiple times. -93: [17:55:19] product atom-mapping number 4 found multiple times. -93: [17:55:19] product atom-mapping number 5 found multiple times. -93: [17:55:19] product atom-mapping number 6 found multiple times. -93: [17:55:19] product atom-mapping number 7 found multiple times. -93: [17:55:19] product atom-mapping number 8 found multiple times. -93: [17:55:19] product atom-mapping number 12 found multiple times. -93: [17:55:19] product atom-mapping number 9 found multiple times. -93: [17:55:19] product atom-mapping number 10 found multiple times. -93: [17:55:19] product atom-mapping number 11 found multiple times. -93: [17:55:19] reactant 0 has no mapped atoms. -93: [17:55:19] reactant 1 has no mapped atoms. -93: [17:55:19] reactant 3 has no mapped atoms. -93: [17:55:19] reactant atom-mapping number 19 found multiple times. -93: [17:55:19] reactant atom-mapping number 25 found multiple times. -93: [17:55:19] reactant atom-mapping number 20 found multiple times. -93: [17:55:19] reactant atom-mapping number 21 found multiple times. -93: [17:55:19] reactant atom-mapping number 22 found multiple times. -93: [17:55:19] reactant atom-mapping number 23 found multiple times. -93: [17:55:19] reactant atom-mapping number 24 found multiple times. -93: [17:55:19] product atom-mapping number 1 found multiple times. -93: [17:55:19] product atom-mapping number 1 found multiple times. -93: [17:55:19] product atom-mapping number 1 found multiple times. -93: [17:55:19] product atom-mapping number 1 found multiple times. -93: [17:55:19] product atom-mapping number 2 found multiple times. -93: [17:55:19] product atom-mapping number 1 found multiple times. -93: [17:55:19] product atom-mapping number 2 found multiple times. -93: [17:55:19] product atom-mapping number 1 found multiple times. - 67/236 Test #21: testPyGeometry ......................... Passed 2.79 sec - 68/236 Test #46: graphmolTestsCatch ..................... Passed 2.37 sec -test 109 - Start 109: testFragCatalog - -109: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog -109: Test timeout computed to be: 1500 -test 110 - Start 110: pyFragCatalog - -110: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/FragCatalog/Wrap/rough_test.py" -110: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap -110: Test timeout computed to be: 1500 - 69/236 Test #72: testMolSupplier ........................ Passed 0.30 sec -93: [17:55:19] product atom-mapping number 2 found multiple times. -93: [17:55:19] product atom-mapping number 1 found multiple times. -93: [17:55:19] product atom-mapping number 2 found multiple times. -93: [17:55:19] product atom-mapping number 1 found multiple times. -93: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br -93: [17:55:19] product atom-mapping number 2 found multiple times. -93: [17:55:19] product atom-mapping number 1 found multiple times. -93: [17:55:19] product atom-mapping number 2 found multiple times. -93: [17:55:19] product atom-mapping number 1 found multiple times. -93: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br -93: [17:55:19] product atom-mapping number 5 found multiple times. -93: [17:55:19] product atom-mapping number 2 found multiple times. -93: [17:55:19] product atom-mapping number 3 found multiple times. -93: [17:55:19] product atom-mapping number 1 found multiple times. -93: [17:55:19] product atom-mapping number 4 found multiple times. -93: [17:55:19] product atom-mapping number 5 found multiple times. -93: [17:55:19] product atom-mapping number 2 found multiple times. -93: [17:55:19] product atom-mapping number 3 found multiple times. -93: [17:55:19] product atom-mapping number 1 found multiple times. -93: [17:55:19] product atom-mapping number 4 found multiple times. -93: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br -93: [17:55:19] product atom-mapping number 5 found multiple times. -93: [17:55:19] product atom-mapping number 2 found multiple times. -93: [17:55:19] product atom-mapping number 3 found multiple times. -93: [17:55:19] product atom-mapping number 1 found multiple times. -93: [17:55:19] product atom-mapping number 4 found multiple times. -93: [17:55:19] product atom-mapping number 5 found multiple times. -93: [17:55:19] product atom-mapping number 2 found multiple times. -93: [17:55:19] product atom-mapping number 3 found multiple times. -93: [17:55:19] product atom-mapping number 1 found multiple times. -93: [17:55:19] product atom-mapping number 4 found multiple times. -93: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br -93: [17:55:19] product atom-mapping number 2 found multiple times. -93: [17:55:19] product atom-mapping number 3 found multiple times. -93: [17:55:19] product atom-mapping number 1 found multiple times. -93: [17:55:19] product atom-mapping number 4 found multiple times. -93: [17:55:19] product atom-mapping number 2 found multiple times. -93: [17:55:19] product atom-mapping number 3 found multiple times. -93: [17:55:19] product atom-mapping number 1 found multiple times. -93: [17:55:19] product atom-mapping number 4 found multiple times. -93: F[C@@](Cl)(Br)O[C@](F)(Cl)Br -93: [17:55:19] product atom-mapping number 2 found multiple times. -93: [17:55:19] product atom-mapping number 3 found multiple times. -93: [17:55:19] product atom-mapping number 1 found multiple times. -93: [17:55:19] product atom-mapping number 4 found multiple times. -93: [17:55:19] product atom-mapping number 2 found multiple times. -93: [17:55:19] product atom-mapping number 3 found multiple times. -93: [17:55:19] product atom-mapping number 1 found multiple times. -93: [17:55:19] product atom-mapping number 4 found multiple times. -93: F[C@](Cl)(Br)O[C@](F)(Cl)Br -93: [17:55:19] product atom-mapping number 4 found multiple times. -93: [17:55:19] product atom-mapping number 3 found multiple times. -93: [17:55:19] product atom-mapping number 2 found multiple times. -93: [17:55:19] product atom-mapping number 1 found multiple times. -93: [17:55:19] product atom-mapping number 4 found multiple times. -93: [17:55:19] product atom-mapping number 3 found multiple times. -93: [17:55:19] product atom-mapping number 2 found multiple times. -93: [17:55:19] product atom-mapping number 1 found multiple times. -93: [17:55:19] product atom-mapping number 4 found multiple times. -93: [17:55:19] product atom-mapping number 3 found multiple times. -93: [17:55:19] product atom-mapping number 2 found multiple times. -93: [17:55:19] product atom-mapping number 1 found multiple times. -93: [17:55:19] product atom-mapping number 4 found multiple times. -93: [17:55:19] product atom-mapping number 3 found multiple times. -93: [17:55:19] product atom-mapping number 2 found multiple times. -93: [17:55:19] product atom-mapping number 1 found multiple times. -93: [17:55:19] product atom-mapping number 3 found multiple times. -93: [17:55:19] product atom-mapping number 2 found multiple times. -93: [17:55:19] product atom-mapping number 1 found multiple times. -93: [17:55:19] mapped atoms in the reactants were not mapped in the products. -93: unmapped numbers are: 4 -93: [17:55:19] product atom-mapping number 3 found multiple times. -93: [17:55:19] product atom-mapping number 2 found multiple times. -93: [17:55:19] product atom-mapping number 1 found multiple times. -93: [17:55:19] mapped atoms in the reactants were not mapped in the products. -93: unmapped numbers are: 4 -93: [17:55:19] product atom-mapping number 6 not found in reactants. -93: [17:55:19] product atom-mapping number 7 not found in reactants. -93: [17:55:19] product atom-mapping number 8 not found in reactants. -93: [17:55:19] product atom-mapping number 7 not found in reactants. -93: [17:55:19] product atom-mapping number 8 not found in reactants. -93: [17:55:19] product atom-mapping number 9 not found in reactants. -93: [17:55:19] product atom-mapping number 10 not found in reactants. -93: [17:55:19] mapped atoms in the reactants were not mapped in the products. -93: unmapped numbers are: 6 -93: [17:55:19] product atom-mapping number 7 not found in reactants. -93: [17:55:19] product atom-mapping number 8 not found in reactants. -93: [17:55:19] product atom-mapping number 9 not found in reactants. -93: [17:55:19] product atom-mapping number 10 not found in reactants. -93: [17:55:19] mapped atoms in the reactants were not mapped in the products. -93: unmapped numbers are: 6 - 70/236 Test #94: testReactionFingerprints ............... Passed 0.08 sec - 71/236 Test #2: pyCoordGen ............................. Passed 2.83 sec -90: hits: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 -90: processing -90: launch :0 -90: launch :1 -90: launch :2 -90: launch :3 -35: [17:55:19] ----------------------- -35: Testing isRingFused - 72/236 Test #35: graphmolMolOpsTest ..................... Passed 2.77 sec -96: Randomness seeded to: 1237313234 -96: [17:55:19] atom 0 in product 0 has multiple charge specifications. -96: [17:55:19] Found a SCD/SED line with missing/empty SDT specification at line 34 -96: [17:55:19] Found a SCD/SED line with missing/empty SDT specification at line 36 -96: [17:55:19] Found a SCD/SED line with missing/empty SDT specification at line 38 -96: [17:55:19] Found a SCD/SED line with missing/empty SDT specification at line 40 -96: [17:55:19] Found a SCD/SED line with missing/empty SDT specification at line 42 -96: [17:55:19] Found a SCD/SED line with missing/empty SDT specification at line 87 -96: [17:55:19] Found a SCD/SED line with missing/empty SDT specification at line 89 -96: [17:55:19] Found a SCD/SED line with missing/empty SDT specification at line 91 -96: [17:55:19] Found a SCD/SED line with missing/empty SDT specification at line 93 -96: [17:55:19] Found a SCD/SED line with missing/empty SDT specification at line 95 -96: [17:55:19] mapped atoms in the reactants were not mapped in the products. + 70/236 Test #58: smiTest1 ............................... Passed 1.10 sec + 71/236 Test #83: cdxmlParserCatchTest ................... Passed 0.56 sec +60: Test +60: +60: JDQ443_3d.cxsmi +60: +60: Test +60: +60: JDQ443_atrop1.cxsmi +60: +60: Test +60: +60: JDQ443_atrop2.cxsmi +60: +60: Test +60: +60: JDQ443_atrop3.cxsmi +60: +60: Test +60: +60: JDQ443_atrop4.cxsmi +60: +60: Test +60: +60: JDQ443_atropBad1.cxsmi +60: +60: [14:17:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +60: [14:17:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +60: [14:17:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +60: [14:17:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +60: [14:17:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +60: Test +60: +60: RP-6306_atrop1.cxsmi +60: +60: Test +60: +60: RP-6306_atrop2.cxsmi +60: +60: Test +60: +60: RP-6306_atrop3.cxsmi +60: +60: Test +60: +60: RP-6306_atrop4.cxsmi +60: +60: Test +60: +60: RP-6306_atrop5.cxsmi +60: +60: [14:17:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [14:17:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [14:17:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [14:17:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [14:17:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [14:17:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [14:17:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [14:17:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [14:17:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [14:17:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +96: Randomness seeded to: 16917691 +96: [14:17:38] atom 0 in product 0 has multiple charge specifications. +96: [14:17:38] Found a SCD/SED line with missing/empty SDT specification at line 34 +96: [14:17:38] Found a SCD/SED line with missing/empty SDT specification at line 36 +96: [14:17:38] Found a SCD/SED line with missing/empty SDT specification at line 38 +96: [14:17:38] Found a SCD/SED line with missing/empty SDT specification at line 40 +96: [14:17:38] Found a SCD/SED line with missing/empty SDT specification at line 42 +96: [14:17:38] Found a SCD/SED line with missing/empty SDT specification at line 87 +96: [14:17:38] Found a SCD/SED line with missing/empty SDT specification at line 89 +96: [14:17:38] Found a SCD/SED line with missing/empty SDT specification at line 91 +96: [14:17:38] Found a SCD/SED line with missing/empty SDT specification at line 93 +96: [14:17:38] Found a SCD/SED line with missing/empty SDT specification at line 95 +96: [14:17:38] mapped atoms in the reactants were not mapped in the products. 96: unmapped numbers are: 2 -96: [17:55:19] mapped atoms in the reactants were not mapped in the products. +96: [14:17:38] mapped atoms in the reactants were not mapped in the products. 96: unmapped numbers are: 2 -96: [17:55:19] SMARTS Parse Error: unclosed ring for input: 'CC1' -96: [17:55:19] SMILES Parse Error: unclosed ring for input: 'CC1' -96: [17:55:19] mapped atoms in the reactants were not mapped in the products. +96: [14:17:38] SMARTS Parse Error: unclosed ring for input: 'CC1' +96: [14:17:38] SMILES Parse Error: unclosed ring for input: 'CC1' +96: [14:17:38] mapped atoms in the reactants were not mapped in the products. 96: unmapped numbers are: 2 -96: [17:55:19] product atom-mapping number 2 not found in reactants. -96: [17:55:19] mapped atoms in the reactants were not mapped in the products. +96: [14:17:38] product atom-mapping number 2 not found in reactants. +96: [14:17:38] mapped atoms in the reactants were not mapped in the products. 96: unmapped numbers are: 2 -96: [17:55:19] product atom-mapping number 2 not found in reactants. -96: [17:55:19] CX Extensions: Substance group hierarchy is not always preserved. -96: [17:55:19] CX Extensions: Substance group hierarchy is not always preserved. +96: [14:17:38] product atom-mapping number 2 not found in reactants. +96: [14:17:38] CX Extensions: Substance group hierarchy is not always preserved. +96: [14:17:38] CX Extensions: Substance group hierarchy is not always preserved. +96: [14:17:38] reactant 0 has no mapped atoms. +96: [14:17:38] product 0 has no mapped atoms. +96: [14:17:38] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +96: [14:17:38] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +96: [14:17:38] Explicit valence for atom # 1 O, 5, is greater than permitted +96: =============================================================================== +96: All tests passed (722 assertions in 30 test cases) +96: +35: [14:17:38] Maximum BFS search size exceeded. +35: This is likely due to a highly symmetric fused ring system. + 72/236 Test #30: pyForceFieldConstraints ................ Passed 1.62 sec 100: 1 smi: CC 100: 1 smi: CC 100: 2 smi: CCO[C@H](N)P @@ -21010,22 +20761,14 @@ 100: replaceSub smi1:CCNCC 100: sidechains chiral=true smi1;;; [1*]P([2*])[C@H](N)O 100: sidechains chiral=false smi1;;; [1*]P([2*])[C@H](N)O -104: ----------------------- -104: Subgraph retrieval -104: Finished -104: ----------------------- -104: testSubgraphs2a -104: Finished -104: ----------------------- -104: testSubgraphs2 -105: ----------------------- -105: Test1: pathToSubmol -105: Finished -105: ----------------------- -105: Test2: Atom Environments -105: Finished -105: ----------------------- -105: Test 3: Atom Environments (Extension) +100: [14:17:38] SMARTS Parse Error: syntax error while parsing: bar +100: [14:17:38] SMARTS Parse Error: Failed parsing SMARTS 'bar' for input: 'bar' +test 110 + Start 110: pyFragCatalog + +110: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/FragCatalog/Wrap/rough_test.py" +110: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap +110: Test timeout computed to be: 1500 test 111 Start 111: testDescriptors @@ -21038,65 +20781,157 @@ 112: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testAUTOCORR2D 112: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 112: Test timeout computed to be: 1500 -test 113 - Start 113: testATF - -113: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testATF -113: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -113: Test timeout computed to be: 1500 -test 114 - Start 114: testBCUT - -114: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testBCUT -114: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -114: Test timeout computed to be: 1500 -93: 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] -93: 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] -60: Test -60: -60: Sotorasib_3d.cxsmi -60: -60: Test -60: -60: ZM374979_atrop1.cxsmi -60: -60: Test -60: -60: ZM374979_atrop2.cxsmi -60: -60: Test -60: -60: ZM374979_atrop3.cxsmi -60: -60: Test -60: -60: ZM374979_atrop4.cxsmi -60: -60: Test -60: -60: ZM374979_atropBad1.cxsmi -60: -60: [17:55:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -60: [17:55:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -60: [17:55:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -60: [17:55:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -60: [17:55:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -83: [17:55:19] Incomplete atom labelling, cannot make bond -83: [17:55:19] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas -83: [17:55:19] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas -83: [17:55:19] Failed to parse XML fragment 5 node: b attribute: Order: slartibartfast -83: [17:55:19] Failed to parse XML fragment 5 node: b attribute: Order: 5 -83: [17:55:19] Invalid or missing fragment id from CDXML fragment, assigning new one... -105: Finished -105: ----------------------- -105: Testing github Issue103: stereochemistry and pathToSubmol -105: Finished -105: ----------------------- -105: Testing github Issue103: more stereochemistry and pathToSubmol (path needs to be in sorted order) -105: Finished -101: Randomness seeded to: 3871182915 -101: [17:55:19] Incomplete atom labelling, cannot make bond -101: [17:55:19] + 73/236 Test #96: rxnTestCatch ........................... Passed 0.40 sec + 74/236 Test #100: testChemTransforms ..................... Passed 0.26 sec +93: [14:17:38] mapped atoms in the reactants were not mapped in the products. +93: unmapped numbers are: 7 8 9 10 11 12 13 14 15 16 +93: [14:17:38] product atom-mapping number 17 not found in reactants. +93: [14:17:38] product atom-mapping number 18 not found in reactants. +93: [14:17:38] mapped atoms in the reactants were not mapped in the products. +93: unmapped numbers are: 12 +93: [14:17:38] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) +93: [14:17:38] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) +93: +93: [14:17:38] Mismatched potential rlabels: 1 unmapped reactant dummy atom rlabels,0 unmappped product dummy atom rlabels +93: ------------- +93: CCOc1ccccc1 +72: [14:17:38] Finished: testSDWriter() +72: [14:17:38] ----------------------------------------- +72: +72: [14:17:38] ----------------------------------------- +72: [14:17:38] Finished: testSDSupplierEnding() +72: [14:17:38] ----------------------------------------- +72: +72: [14:17:38] ----------------------------------------- +72: [14:17:38] Finished: testSuppliersEmptyFile() +72: [14:17:38] ----------------------------------------- +72: +72: [14:17:38] ----------------------------------------- +72: [14:17:38] Finished: testCisTrans() +72: [14:17:38] ----------------------------------------- +72: +72: [14:17:38] ----------------------------------------- +72: [14:17:38] Finished: testStereoRound() +72: [14:17:38] ----------------------------------------- +72: +72: [14:17:38] ----------------------------------------- +72: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +72: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +72: [14:17:38] Finished: testIssue226() +72: [14:17:38] ----------------------------------------- +72: +72: [14:17:38] ----------------------------------------- +72: [14:17:38] Finished: testTDTSupplier1() +72: [14:17:38] ----------------------------------------- +72: +72: [14:17:38] ----------------------------------------- +72: [14:17:38] Finished: testTDTSupplier2() +72: [14:17:38] ----------------------------------------- +72: +72: [14:17:38] ----------------------------------------- +72: [14:17:38] Finished: testTDTSupplier3() +72: [14:17:38] ----------------------------------------- +72: +72: [14:17:38] ----------------------------------------- +72: [14:17:38] Finished: testSDSupplierFromText() +72: [14:17:38] ----------------------------------------- +72: +72: [14:17:38] ----------------------------------------- +72: [14:17:38] ERROR: Problems encountered parsing data fields +72: [14:17:38] ERROR: moving to the beginning of the next molecule +72: [14:17:38] ERROR: Problems encountered parsing data fields +72: [14:17:38] ERROR: moving to the beginning of the next molecule +72: [14:17:38] Spurious data before the first property will be ignored +72: [14:17:38] Property will be truncated after the first blank line +72: [14:17:38] Property will be truncated after the first blank line +72: [14:17:38] Property will be truncated after the first blank line +72: [14:17:38] Finished: testSDSupplierStrLax1() +72: [14:17:38] ----------------------------------------- +72: +72: [14:17:38] ----------------------------------------- +72: [14:17:38] ERROR: Problems encountered parsing data fields +72: [14:17:38] ERROR: moving to the beginning of the next molecule +72: [14:17:38] Property will be truncated after the first blank line +72: [14:17:38] Finished: testSDSupplierStrLax2() +72: [14:17:38] ----------------------------------------- +72: +72: [14:17:38] ----------------------------------------- +72: [14:17:38] ERROR: Problems encountered parsing data fields +72: [14:17:38] ERROR: moving to the beginning of the next molecule +72: [14:17:38] ERROR: Problems encountered parsing data fields +72: [14:17:38] ERROR: moving to the beginning of the next molecule +72: [14:17:38] Spurious data before the first property will be ignored +72: [14:17:38] Property will be truncated after the first blank line +72: [14:17:38] Property will be truncated after the first blank line +72: [14:17:38] Property will be truncated after the first blank line +72: [14:17:38] Finished: testSDSupplierFromTextStrLax1() +72: [14:17:38] ----------------------------------------- +72: +72: [14:17:38] ----------------------------------------- +72: [14:17:38] ERROR: Problems encountered parsing data fields +72: [14:17:38] ERROR: moving to the beginning of the next molecule +72: [14:17:38] Property will be truncated after the first blank line +72: [14:17:38] Finished: testSDSupplierFromTextStrLax2() +72: [14:17:38] ----------------------------------------- +72: +72: [14:17:38] ----------------------------------------- +72: [14:17:38] Finished: testIssue265() +72: [14:17:38] ----------------------------------------- +72: +72: [14:17:38] ----------------------------------------- +72: [14:17:38] ERROR: End of data field name not found +72: [14:17:38] ERROR: moving to the beginning of the next molecule +72: [14:17:38] Explicit valence for atom # 0 F, 2, is greater than permitted +72: [14:17:38] ERROR: Could not sanitize molecule ending on line 16 +72: [14:17:38] ERROR: Explicit valence for atom # 0 F, 2, is greater than permitted +72: [14:17:38] ERROR: Atom line too short: ' 1 2 1 0 0 0 0' on line 12 +72: [14:17:38] ERROR: moving to the beginning of the next molecule +72: [14:17:38] ERROR: Bond line too short: 'M END' on line 18 +72: [14:17:38] ERROR: moving to the beginning of the next molecule +72: [14:17:38] Finished: testSDErrorHandling() +72: [14:17:38] ----------------------------------------- +72: +72: [14:17:38] ----------------------------------------- +72: [14:17:38] Finished: testIssue381() +72: [14:17:38] ----------------------------------------- +72: +72: [14:17:38] ----------------------------------------- +72: [14:17:38] Finished: testSetStreamIndices() +72: [14:17:38] ----------------------------------------- +72: +72: [14:17:38] ----------------------------------------- +72: [14:17:38] Finished: testMixIterAndRandom() +72: [14:17:38] ----------------------------------------- +72: +72: [14:17:38] ----------------------------------------- +72: build: +72: [14:17:38] Finished: testRemoveHs() +72: [14:17:38] ----------------------------------------- +72: +72: [14:17:38] ----------------------------------------- +72: [14:17:38] Finished: testGetItemText() +72: [14:17:38] ----------------------------------------- +72: +72: [14:17:38] ----------------------------------------- +70: [14:17:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [14:17:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [14:17:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [14:17:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [14:17:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [14:17:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [14:17:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +70: [14:17:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +70: [14:17:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +70: [14:17:38] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +70: [14:17:38] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +70: [14:17:38] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +70: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +65: [14:17:38] Warning: stereochemistry around double bond may be incorrect in depiction. +101: Randomness seeded to: 3352952649 +101: [14:17:38] Incomplete atom labelling, cannot make bond +101: [14:17:38] 101: 101: **** 101: Invariant Violation @@ -21109,53 +20944,21 @@ 101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 101: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 101: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 -101: 4# 0x0000563FA6996596 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 5# 0x0000563FA69E8168 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x0000563FA69E8C88 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x0000563FA69E9100 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x0000563FA69BA903 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x0000563FA69BAC6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x0000563FA698A75E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x00007F0B37633CA8 in /lib/x86_64-linux-gnu/libc.so.6 +101: 4# 0x00005563ED5BE596 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 5# 0x00005563ED610168 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x00005563ED610C88 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x00005563ED611100 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x00005563ED5E2903 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x00005563ED5E2C6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x00005563ED5B275E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x00007F47E0E33CA8 in /lib/x86_64-linux-gnu/libc.so.6 101: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -101: 13# 0x0000563FA698A7A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 13# 0x00005563ED5B27A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- 101: **** 101: -106: Randomness seeded to: 529914614 -106: --------- -106: =============================================================================== -106: All tests passed (11 assertions in 1 test case) -106: -100: [17:55:19] SMARTS Parse Error: syntax error while parsing: bar -100: [17:55:19] SMARTS Parse Error: Failed parsing SMARTS 'bar' for input: 'bar' -96: [17:55:19] reactant 0 has no mapped atoms. -96: [17:55:19] product 0 has no mapped atoms. -96: [17:55:19] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -96: [17:55:19] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -96: [17:55:19] Explicit valence for atom # 1 O, 5, is greater than permitted -96: =============================================================================== -96: All tests passed (722 assertions in 30 test cases) -96: - 73/236 Test #105: testSubgraphs2 ......................... Passed 0.05 sec - 74/236 Test #106: subgraphsCatch ......................... Passed 0.04 sec -test 115 - Start 115: testEEM - -115: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testEEM -115: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -115: Test timeout computed to be: 1500 -test 116 - Start 116: testPBF - -116: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testPBF -116: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -116: Test timeout computed to be: 1500 -83: =============================================================================== -83: All tests passed (263 assertions in 7 test cases) -83: -101: [17:55:19] Incomplete atom labelling, cannot make bond -101: [17:55:19] +101: [14:17:38] Incomplete atom labelling, cannot make bond +101: [14:17:38] 101: 101: **** 101: Invariant Violation @@ -21168,395 +20971,98 @@ 101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 101: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 101: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 -101: 4# 0x0000563FA6996596 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 5# 0x0000563FA69E8168 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x0000563FA69E8C88 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x0000563FA69E9100 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x0000563FA69BA903 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x0000563FA69BAC6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x0000563FA698A75E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x00007F0B37633CA8 in /lib/x86_64-linux-gnu/libc.so.6 +101: 4# 0x00005563ED5BE596 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 5# 0x00005563ED610168 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x00005563ED610C88 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x00005563ED611100 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x00005563ED5E2903 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x00005563ED5E2C6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x00005563ED5B275E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x00007F47E0E33CA8 in /lib/x86_64-linux-gnu/libc.so.6 101: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -101: 13# 0x0000563FA698A7A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 13# 0x00005563ED5B27A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- 101: **** 101: -111: [17:55:19] ------------------------------------- -111: [17:55:19] Test Crippen parameter acquisition. -111: [17:55:19] done -111: [17:55:19] ------------------------------------- -111: [17:55:19] Test Crippen calculation. -109: 21 -68: Test -68: -68: badWedgeError.sdf -68: -68: Test -68: -68: CrossedDoubleBondWithChiralNbr2.sdf -68: -68: Test -68: -68: CrossedDoubleBondWithChiralNbr.sdf -68: -68: Test -68: -68: SimpleWiggleDoubleBond.sdf -68: -68: Test -68: -68: lostStereoAnd.sdf -68: -68: Test -68: -68: DoubleBondChain.sdf -68: -68: Test -68: -68: UnitsError.sdf -68: -68: Test -68: -68: StarAtom.sdf -68: -68: Test -68: -68: nonProprietary.mol -68: -68: Test -68: -68: ChiralTest.sdf -68: -68: Test -68: -68: TestBond1.mol -68: -68: Test -68: -68: Sgroup_MUL_ParentInMiddle.sdf -68: -68: Test -68: -68: BadRxn.rxn -68: -68: Test -68: -68: FalseChiral.mrv -68: -68: Test -68: -68: FalseChiral.mrv -68: -68: Test -68: -68: Cubane.mrv -68: -68: Test -68: -68: NewChiralTest.mrv -68: -68: Test -68: -68: NewChiralTest.mrv -68: -68: Test -68: -68: NewChiralTestNoChiral.mrv -68: -68: Test -68: -68: NewChiralTestNoChiral.mrv -68: -68: Test -68: -68: NewChiralTestAllChiral.mrv -68: -68: Test -68: -68: NewChiralTestAllChiral.mrv -68: -68: Test -68: -68: DataSgroupMissingUnitsDisplayed.mrv -68: -68: Test -68: -68: lostStereoAnd.mrv -68: -68: Test -68: -68: DoubleBondChain.mrv -68: -68: Test -68: -68: WigglyAndCrossed.mrv -68: -68: Test -68: -68: BondTypes.mrv -68: -68: Test -68: -68: EmbeddedSGroupSUP_MUL.mrv -68: -68: Test -68: -68: EmbeddedSgroupCOP_SUP.mrv -68: -68: Test -68: -68: EmbeddedSgroupDAT_SUP.mrv -68: -68: Test -68: -68: EmbeddedSgroupMULTICENTER_SUP.mrv -68: -68: Test -68: -68: EmbeddedSgroupMUL_MUL.mrv -68: -68: Test -68: -68: EmbeddedSgroupMUL_MUL2.mrv -68: -68: Test -68: -68: EmbeddedSgroupMUL_SUP.mrv -68: -68: Test -68: -68: EmbeddedSgroupSRU_SUP.mrv -68: -68: Test -68: -68: EmbeddedSgroupSUPEXP_SUP.mrv -68: -68: Test -68: -68: EmbeddedSgroupSUPEXP_SUP2.mrv -68: -68: Test -68: -68: EmbeddedSgroupSUP_MULTICENTER.mrv -68: -68: Test -68: -68: EmbeddedSgroupSUP_SUP.mrv -68: -68: Test -68: -68: EmbeddedSgroupSUP_SUP2.mrv -68: -68: Test -68: -68: RgroupBad.mrv -68: -68: Test -68: -68: valenceLessThanDrawn.mrv -68: -68: Test -68: -68: data_sgroup_no_fieldname.mrv -68: -68: Test -68: -68: data_sgroup_empty_field_data.mrv -68: -68: Test -68: -68: radical_value.mrv -68: -68: Test -68: -68: emptyOneLineAtomList.mrv -68: -68: Test -68: -68: mrvValence_value.mrv -68: -68: Test -68: -68: ChiralTest2.mrv -68: -68: Test -68: -68: ChiralTest.mrv -68: -68: Test -68: -68: SnCl2.mrv -68: -68: Test -68: -68: SnH2Cl2.mrv -68: -68: Test -68: -68: marvin01.mrv -68: -68: Test -68: -68: marvin02.mrv -68: -68: Test -68: -68: marvin07.mrv -68: -68: Test -68: -68: marvin10.mrv -68: -68: Test -68: -68: marvin06.mrv -68: -68: Test -68: -68: marvin12.mrv -68: -68: Test -68: -68: EmptyMol.mrv -68: -68: Test -68: -68: Sparse.mrv -68: -68: Test -68: -68: Sparse2.mrv -68: -68: Test -68: -68: Sparse3.mrv -68: -68: Test -68: -68: MarvinNoCoords.mrv -68: -68: Test -68: -68: aspirin.mrv -68: -68: Test -68: -68: MarvinStereoGroupsZeros.mrv -68: -68: Test -68: -68: MarvinStereoGroupsAbs.mrv -68: -68: Test -68: -68: triphenylphosphine.mrv -68: -68: Test -68: -68: MarvinOldSuperGroupTest.mrv -68: -68: Test -68: -68: RadicalTests.mrv -68: -68: Test -68: -68: AnyBond.mrv -68: -68: Test -68: -68: cisBenzene.mrv -68: -68: Test -68: -68: DativeBond.mrv -68: -68: Test -68: -68: MultipleSgroup.mrv -68: -68: Test -68: -68: SgroupExpanded.mrv -68: -68: Test -68: -68: SgroupMultAttach.mrv -68: -68: Test -68: -68: MarvinMissingX2.mrv -68: -68: Test -68: -68: MarvinMissingY2.mrv -68: -68: Test -68: -68: DataSgroup.mrv -68: -68: Test -68: -68: MulticenterSgroup.mrv -68: -68: [17:55:19] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -68: [17:55:19] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -60: Test -60: -60: Mrtx1719_3d.cxsmi -60: -60: Test -60: -60: Mrtx1719_atrop1.cxsmi -60: -60: Test -60: -60: Mrtx1719_atrop2.cxsmi -60: +104: ----------------------- +104: Subgraph retrieval +104: Finished +104: ----------------------- +104: testSubgraphs2a +104: Finished +104: ----------------------- +104: testSubgraphs2 +105: ----------------------- +105: Test1: pathToSubmol +105: Finished +105: ----------------------- +105: Test2: Atom Environments +105: Finished +105: ----------------------- +105: Test 3: Atom Environments (Extension) +105: Finished +105: ----------------------- +105: Testing github Issue103: stereochemistry and pathToSubmol +105: Finished +105: ----------------------- +105: Testing github Issue103: more stereochemistry and pathToSubmol (path needs to be in sorted order) +105: Finished + 75/236 Test #105: testSubgraphs2 ......................... Passed 0.16 sec +test 113 + Start 113: testATF + +113: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testATF +113: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +113: Test timeout computed to be: 1500 +test 114 + Start 114: testBCUT + +114: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testBCUT +114: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +114: Test timeout computed to be: 1500 +test 115 + Start 115: testEEM + +115: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testEEM +115: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +115: Test timeout computed to be: 1500 60: Test 60: -60: Mrtx1719_atrop3.cxsmi +60: RP-6306_atrop6.cxsmi 60: 60: Test 60: -60: Mrtx1719_atrop4.cxsmi +60: RP-6306_atropBad1.cxsmi 60: +60: [14:17:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +60: [14:17:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +60: [14:17:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +60: [14:17:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +60: [14:17:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 60: Test 60: -60: Mrtx1719_atropBad1.cxsmi +60: RP-6306_atropBad2.cxsmi 60: -60: [17:55:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -60: [17:55:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -60: [17:55:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 - 75/236 Test #83: cdxmlParserCatchTest ................... Passed 0.17 sec - 76/236 Test #96: rxnTestCatch ........................... Passed 0.11 sec -60: [17:55:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -80: [17:55:19] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -test 117 - Start 117: testRDFcustom - -117: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testRDFcustom -117: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -117: Test timeout computed to be: 1500 -test 118 - Start 118: testRDF +60: [14:17:38] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +60: [14:17:38] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +60: [14:17:38] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +60: [14:17:38] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +60: [14:17:38] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +106: Randomness seeded to: 2464686639 +106: --------- +106: =============================================================================== +106: All tests passed (11 assertions in 1 test case) +106: + 76/236 Test #106: subgraphsCatch ......................... Passed 0.19 sec +test 116 + Start 116: testPBF -118: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testRDF -118: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -118: Test timeout computed to be: 1500 -60: [17:55:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -80: [17:55:19] WARNING: atom 1 in input Maestro file has atomic number '0', which is reserved for internal use, and not allowed in inputs. The atom will be ignored.[17:55:19] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -80: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -80: [17:55:19] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -80: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -112: [17:55:19] ---------------------------- -112: start test autocorr2D -114: [17:55:19] ------------------------------------- -114: [17:55:19] Basic BCUT tests. -93: [17:55:19] mapped atoms in the reactants were not mapped in the products. -93: unmapped numbers are: 7 8 9 10 11 12 13 14 15 16 -101: [17:55:19] Incomplete atom labelling, cannot make bond -101: [17:55:19] +116: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testPBF +116: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +116: Test timeout computed to be: 1500 +95: 30000000 30000000 +101: [14:17:38] Incomplete atom labelling, cannot make bond +101: [14:17:38] 101: 101: **** 101: Invariant Violation @@ -21569,119 +21075,23 @@ 101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 101: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 101: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 -101: 4# 0x0000563FA6996596 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 5# 0x0000563FA69E8168 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x0000563FA69E8C88 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x0000563FA69E9100 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x0000563FA69BA903 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x0000563FA69BAC6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x0000563FA698A75E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x00007F0B37633CA8 in /lib/x86_64-linux-gnu/libc.so.6 +101: 4# 0x00005563ED5BE596 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 5# 0x00005563ED610168 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x00005563ED610C88 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x00005563ED611100 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x00005563ED5E2903 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x00005563ED5E2C6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x00005563ED5B275E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x00007F47E0E33CA8 in /lib/x86_64-linux-gnu/libc.so.6 101: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -101: 13# 0x0000563FA698A7A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 13# 0x00005563ED5B27A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- 101: **** 101: -111: [17:55:19] done -111: [17:55:19] ------------------------------------- -111: [17:55:19] Test Issue262: problems with Crippen calculation from pickles. -111: [17:55:19] done -111: [17:55:19] ------------------------------------- -111: [17:55:19] Test AMW calculation. -111: [17:55:19] done -111: [17:55:19] ------------------------------------- -111: [17:55:19] Test Exact MW calculation. -111: [17:55:19] done -111: [17:55:19] ------------------------------------- -111: [17:55:19] Test Labute ASA descriptors. -111: [17:55:19] done -111: [17:55:19] ------------------------------------- -111: [17:55:19] Test TPSA descriptors. -68: Test -68: -68: GenericSgroup.mrv -68: -68: Test -68: -68: MonomerSgroup.mrv -68: -68: Test -68: -68: modification_sgroup.mrv -68: -68: Test -68: -68: copolymer_sgroup.mrv -68: -68: Test -68: -68: MultipleSgroupParentInMiddleOfAtomBlock.mrv -68: -68: Test -68: -68: EmbeddedSgroups.mrv -68: -68: Test -68: -68: marvin03.mrv -68: -68: Test -68: -68: MarvinBadMissingMolID.mrv -68: -68: [17:55:19] -68: -68: **** -116: [17:55:19] ------------------------------------- -116: [17:55:19] Basic PBF tests. -68: Test Assert -68: Expression Failed: -68: Violation occurred on line 329 in file ./Code/GraphMol/MarvinParse/testMrvToMol.cpp -68: Failed Expression: GetExpectedValue(expectedMrvName) == outMolStr -68: ---------- -68: Stacktrace: -68: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -68: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -68: 2# 0x000055D0457A799F in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol -68: 3# 0x000055D0457B269C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol -68: 4# 0x000055D04579FA5D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol -68: 5# 0x00007FDB3F633CA8 in /lib/x86_64-linux-gnu/libc.so.6 -68: 6# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -68: 7# 0x000055D04579FBE1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol -68: ---------- -68: **** -68: -68: Test -68: -68: MarvinBadMissingAtomID.mrv -68: -68: Expected id, elementType for an atom definition in MRV file - 77/236 Test #100: testChemTransforms ..................... Passed 0.10 sec -test 119 - Start 119: testMORSE - -119: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testMORSE -119: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -119: Test timeout computed to be: 1500 -68: Test -68: -68: MarvinBadX2.mrv -68: -68: The values x2 and y2 must be large floats in MRV file -68: Test -68: -68: MarvinBadY2.mrv -68: -68: The values x2 and y2 must be large floats in MRV file -101: [17:55:19] Incomplete atom labelling, cannot make bond -68: Test -68: -68: MarvinBadStereoGroupsAbs.mrv -68: -68: Unrecognized group definition -101: [17:55:19] Incomplete atom labelling, cannot make bond -101: [17:55:19] Incomplete atom labelling, cannot make bond -101: [17:55:19] +101: [14:17:38] Incomplete atom labelling, cannot make bond +101: [14:17:38] Incomplete atom labelling, cannot make bond +101: [14:17:38] Incomplete atom labelling, cannot make bond +101: [14:17:38] 101: 101: **** 101: Invariant Violation @@ -21694,157 +21104,128 @@ 101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 101: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 101: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 -101: 4# 0x0000563FA6996596 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 5# 0x0000563FA69E8168 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x0000563FA69E8C88 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x0000563FA69E9100 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x0000563FA69BA903 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x0000563FA69BAC6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x0000563FA698A75E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x00007F0B37633CA8 in /lib/x86_64-linux-gnu/libc.so.6 +101: 4# 0x00005563ED5BE596 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 5# 0x00005563ED610168 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x00005563ED610C88 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x00005563ED611100 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x00005563ED5E2903 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x00005563ED5E2C6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x00005563ED5B275E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x00007F47E0E33CA8 in /lib/x86_64-linux-gnu/libc.so.6 101: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -101: 13# 0x0000563FA698A7A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 13# 0x00005563ED5B27A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- -68: Test -68: -68: MarvinBadElementType.mrv -68: -68: Test -68: -68: MarvinBadMissingBondID.mrv -68: -68: Test -68: -68: MarvinBadMissingBondAtomRefs -68: -68: Test -68: -68: MarvinBadMissingBondOrder.mrv -68: -68: bond must have one of: order, queryType, or convention in MRV File 101: **** 101: -70: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -68: Test -68: -68: MarvinBadMissingSruMolID.mrv -68: -68: Expected a molID in MRV file -68: Test -68: -68: MarvinBadMissingSruID.mrv -68: -68: Test -68: -68: MarvinBadMissingSruRole.mrv -68: -68: Test -68: -68: MarvinBadMissingSruAtomRef.mrv -68: -68: Test -68: -68: MarvinBadMissingSruTitle.mrv -68: -68: Test -68: -68: MarvinBadSruAtomRef.mrv -68: -68: AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent -115: =>start test EEM -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -68: Test -68: -68: MarvinBadSruID.mrv -68: -68: Test -68: -68: MarvinBadSruRole.mrv -68: -68: Test -68: -68: MarvinBadSruAtomRef.mrv -68: -68: AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent -115: 0 -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -68: Test -68: -68: MarvinBadSruAtomRef.mrv -68: -68: AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent - 78/236 Test #113: testATF ................................ Passed 0.05 sec -test 120 - Start 120: test3D - -120: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/test3D -120: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -120: Test timeout computed to be: 1500 -68: Test -68: -68: MarvinBadSruConnect.mrv -68: -68: Expected a connect string of "hh, ht, eu" for a SruSgroup definition in MRV file -68: Test -68: -68: MarvinBadSupAttachAtom.mrv -68: -68: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file -68: Test -68: -68: MarvinBadSupAttachBond.mrv -68: -68: Bond specification for an AttachmentPoint definition must be in the bond array in MRV file -68: Test -68: -68: MarvinBadSupAttachOrder.mrv -68: -68: Order for an AttachmentPoint definition must be an integer in MRV file -68: Test -68: -68: MarvinBadSupAttachAtom.mrv -68: -68: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -114: [17:55:19] done -114: [17:55:19] ------------------------------------- -114: [17:55:19] Larger BCUT tests. -68: Test -68: -68: MarvinBadSupAttachAtom.mrv -68: -68: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file -68: Test -68: -68: MarvinBadSupAttachAtom.mrv -68: -68: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file -68: Test -68: -68: MarvinBadSupMissingAttachBond.mrv -68: -68: No attachment point found for bond to the condensed atom in a superatomSgroup -68: Test -68: -68: MarvinBadSupMissingAttachOrder.mrv -68: -68: Expected atom, order and bond, for an AttachmentPoint definition in MRV file -93: [17:55:19] product atom-mapping number 17 not found in reactants. -93: [17:55:19] product atom-mapping number 18 not found in reactants. -93: [17:55:19] mapped atoms in the reactants were not mapped in the products. -93: unmapped numbers are: 12 -101: [17:55:19] Incomplete atom labelling, cannot make bond -101: [17:55:19] +70: [14:17:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +70: [14:17:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +70: [14:17:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +70: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +111: [14:17:38] ------------------------------------- +111: [14:17:38] Test Crippen parameter acquisition. +111: [14:17:38] done +111: [14:17:38] ------------------------------------- +111: [14:17:38] Test Crippen calculation. +111: [14:17:38] done +111: [14:17:38] ------------------------------------- +111: [14:17:38] Test Issue262: problems with Crippen calculation from pickles. +111: [14:17:38] done +111: [14:17:38] ------------------------------------- +111: [14:17:38] Test AMW calculation. +111: [14:17:38] done +111: [14:17:38] ------------------------------------- +111: [14:17:38] Test Exact MW calculation. +111: [14:17:38] done +111: [14:17:38] ------------------------------------- +111: [14:17:38] Test Labute ASA descriptors. +111: [14:17:38] done +111: [14:17:38] ------------------------------------- +111: [14:17:38] Test TPSA descriptors. +90: done +90: hits2: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 +90: processing2 +90: launch2 :0 +90: launch2 :1 +90: launch2 :2 +90: launch2 :3 +80: [14:17:38] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +80: [14:17:38] WARNING: atom 1 in input Maestro file has atomic number '0', which is reserved for internal use, and not allowed in inputs. The atom will be ignored.[14:17:38] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +80: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +80: [14:17:38] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +80: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +72: [14:17:38] Finished: testForwardSDSupplier() +72: [14:17:38] ----------------------------------------- +72: +72: [14:17:38] ----------------------------------------- +72: [14:17:38] Finished: testMissingCRSDSupplier() +72: [14:17:38] ----------------------------------------- +72: +72: [14:17:38] ----------------------------------------- +72: [14:17:38] Finished: testIssue3482695() +72: [14:17:38] ----------------------------------------- +72: +72: [14:17:38] ----------------------------------------- +72: [14:17:38] ERROR: Cannot convert 'foo' to unsigned int on line 557 +72: [14:17:38] ERROR: moving to the beginning of the next molecule +112: [14:17:38] ---------------------------- +112: start test autocorr2D +109: 21 +72: [14:17:38] Finished: testIssue3525673() +72: [14:17:38] ----------------------------------------- +72: +72: [14:17:38] ----------------------------------------- +75: [14:17:38] 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: [14:17:38] Finished: testBlankLinesInProps() +72: [14:17:38] ----------------------------------------- +72: +72: [14:17:38] ----------------------------------------- +72: [14:17:38] Finished: testSkipLines() +72: [14:17:38] ----------------------------------------- +72: +72: [14:17:38] ----------------------------------------- +72: [14:17:38] Finished: testGitHub23() +72: [14:17:38] ----------------------------------------- +72: +72: [14:17:38] ----------------------------------------- +75: 0.40201265 0.40201265 +75: -0.13299436 -0.13299436 +75: 1.00000017 1.00000017 +75: 0.8762226 0.8762226 +75: 0.9973909 0.9973909 +75: 1.00000003 1.00000003 +75: 0.36613799 0.36613799 +75: 2.1107185 2.1107185 +75: 0.99999982 0.99999982 +75: 2.48696157 2.48696157 +75: 1.00479935 1.00479935 +75: 0.99999999 0.99999999 +75: 3.03311841 3.03311841 +75: 2.23739955 2.23739955 +75: 1.0000001 1.0000001 +75: 3.00772337 3.00772337 +75: 0.37399294 0.37399294 +75: 2.07713325 2.07713325 +75: 3.0077234 3.0077234 +75: 0.37399312 0.37399312 +75: -0.07713336 -0.07713336 +90: done +90: preprocessing 3 +72: [14:17:38] Finished: testGitHub88() +72: [14:17:38] ----------------------------------------- +72: +72: [14:17:38] ----------------------------------------- +114: [14:17:38] ------------------------------------- +114: [14:17:38] Basic BCUT tests. +90: hits3: 1110100011001000010011100110100011011000010101000100110010101111011100101000001111110000010100100110 +90: processing3 +90: launch3 :0 +90: launch3 :1 +90: launch3 :2 +90: launch3 :3 +101: [14:17:38] Incomplete atom labelling, cannot make bond +101: [14:17:38] 101: 101: **** 101: Invariant Violation @@ -21857,20 +21238,32 @@ 101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 101: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 101: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 -101: 4# 0x0000563FA6996596 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 5# 0x0000563FA69E8168 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x0000563FA69E8C88 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x0000563FA69E9100 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x0000563FA69BA903 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x0000563FA69BAC6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x0000563FA698A75E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x00007F0B37633CA8 in /lib/x86_64-linux-gnu/libc.so.6 +101: 4# 0x00005563ED5BE596 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 5# 0x00005563ED610168 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x00005563ED610C88 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x00005563ED611100 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x00005563ED5E2903 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x00005563ED5E2C6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x00005563ED5B275E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x00007F47E0E33CA8 in /lib/x86_64-linux-gnu/libc.so.6 101: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -101: 13# 0x0000563FA698A7A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 13# 0x00005563ED5B27A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- 101: **** 101: -101: [17:55:19] +116: [14:17:38] ------------------------------------- +116: [14:17:38] Basic PBF tests. + 77/236 Test #113: testATF ................................ Passed 0.10 sec +test 117 + Start 117: testRDFcustom + +117: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testRDFcustom +117: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +117: Test timeout computed to be: 1500 +70: [14:17:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +75: [14:17:38] bond with order 0 found on line 11. This is not part of the MDL specification. +75: [14:17:38] bond with order 0 found on line 16. This is not part of the MDL specification. +101: [14:17:38] 101: 101: **** 101: Invariant Violation @@ -21884,20 +21277,93 @@ 101: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 101: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 101: 4# RDKit::molzip(RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 -101: 5# 0x0000563FA698B87D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x0000563FA69E8168 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x0000563FA69E8C88 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x0000563FA69E9100 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x0000563FA69BA903 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x0000563FA69BAC6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x0000563FA698A75E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 12# 0x00007F0B37633CA8 in /lib/x86_64-linux-gnu/libc.so.6 +101: 5# 0x00005563ED5B387D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x00005563ED610168 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x00005563ED610C88 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x00005563ED611100 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x00005563ED5E2903 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x00005563ED5E2C6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x00005563ED5B275E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 12# 0x00007F47E0E33CA8 in /lib/x86_64-linux-gnu/libc.so.6 101: 13# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -101: 14# 0x0000563FA698A7A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 14# 0x00005563ED5B27A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- 101: **** 101: -95: 30000000 30000000 +70: [14:17:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +70: [14:17:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +101: =============================================================================== +101: All tests passed (675 assertions in 10 test cases) +101: + 78/236 Test #101: chemTransformsTestCatch ................ Passed 0.37 sec +test 118 + Start 118: testRDF + +118: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testRDF +118: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +118: Test timeout computed to be: 1500 +72: [14:17:38] Finished: testGitHub2285() +72: [14:17:38] ----------------------------------------- +72: +72: [14:17:38] ----------------------------------------- +72: [14:17:38] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +72: [14:17:38] ERROR: Smiles parse error on line 1 +72: [14:17:38] ERROR: Cannot create molecule from : 'c1ccccc' +72: [14:17:38] SMILES Parse Error: extra open parentheses while parsing: C(C +72: [14:17:38] SMILES Parse Error: check for mistakes around position 2: +72: [14:17:38] C(C +72: [14:17:38] ~^ +72: [14:17:38] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' +72: [14:17:38] ERROR: Smiles parse error on line 3 +72: [14:17:38] ERROR: Cannot create molecule from : 'C(C' +72: [14:17:38] Explicit valence for atom # 1 C, 5, is greater than permitted +72: [14:17:38] ERROR: Could not sanitize molecule on line 5 +72: [14:17:38] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted +72: [14:17:38] Explicit valence for atom # 1 F, 2, is greater than permitted +72: [14:17:38] ERROR: Could not sanitize molecule ending on line 21 +72: [14:17:38] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +72: [14:17:38] Explicit valence for atom # 1 F, 2, is greater than permitted +72: [14:17:38] ERROR: Could not sanitize molecule ending on line 21 +72: [14:17:38] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +72: [14:17:38] Explicit valence for atom # 1 F, 2, is greater than permitted +72: [14:17:38] ERROR: Could not sanitize molecule ending on line 21 +72: [14:17:38] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +72: [14:17:38] ERROR: Atom line too short: ' -9.6' on line 28 +72: [14:17:38] ERROR: moving to the beginning of the next molecule +72: [14:17:38] Explicit valence for atom # 1 F, 2, is greater than permitted +72: [14:17:38] ERROR: Could not sanitize molecule ending on line 21 +72: [14:17:38] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +72: [14:17:38] ERROR: Atom line too short: ' -9.6' on line 28 +72: [14:17:38] ERROR: moving to the beginning of the next molecule +72: [14:17:38] Finished: testGitHub2479() +72: [14:17:38] ----------------------------------------- +72: +72: [14:17:38] ----------------------------------------- + 79/236 Test #65: testDepictor ........................... Passed 1.10 sec +test 119 + Start 119: testMORSE + +119: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testMORSE +119: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +119: Test timeout computed to be: 1500 +72: [14:17:38] Ignoring invalid chirality label: '7_S_8_9_6_10' +72: [14:17:38] Finished: testGitHub2881() +72: [14:17:38] ----------------------------------------- +72: +72: [14:17:38] ----------------------------------------- +72: [14:17:38] Finished: testGitHub3517() +72: [14:17:38] ----------------------------------------- +72: +114: [14:17:38] done +114: [14:17:38] ------------------------------------- +114: [14:17:38] Larger BCUT tests. + 80/236 Test #72: testMolSupplier ........................ Passed 0.98 sec +test 120 + Start 120: test3D + +120: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/test3D +120: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +120: Test timeout computed to be: 1500 104: Finished 104: ----------------------- 104: Path retrieval @@ -21910,29 +21376,42 @@ 104: Finished 104: ----------------------- 104: testUniqueSubgraphs2 -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -101: =============================================================================== -101: All tests passed (675 assertions in 10 test cases) -101: -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 79/236 Test #101: chemTransformsTestCatch ................ Passed 0.12 sec +115: =>start test EEM +115: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: 0 +115: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +102: Randomness seeded to: 2246646626 +102: =============================================================================== +102: All tests passed (93 assertions in 13 test cases) +102: +93: [14:17:38] reactant 0 has no mapped atoms. +93: [14:17:38] product 0 has no mapped atoms. +93: [14:17:38] WARNING: neither stereo atoms nor CIP codes found for double bond. Stereochemistry info will not be propagated to product. + 81/236 Test #75: testMolWriter .......................... Passed 0.94 sec + 82/236 Test #102: tautomerQueryTestCatch ................. Passed 0.41 sec +115: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. test 121 Start 121: testWHIM 121: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testWHIM 121: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 121: Test timeout computed to be: 1500 -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +test 122 + Start 122: testGETAWAY + +122: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testGETAWAY +122: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +122: Test timeout computed to be: 1500 +115: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 107: Warning: molecule failed filter 107: Warning: molecule failed filter: reason hzone_phenol_A(479) -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 107: v = { 107: 0,23}, 107: 1,22}, @@ -21989,13 +21468,7 @@ 107: 11,17}, 107: 12,16}, 107: } -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 107: Warning: molecule failed filter -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -120: [17:55:19] ------------------------------------- -120: [17:55:19] Basic PMI tests. 107: Warning: molecule failed filter: reason keto_keto_gamma(5) 107: v = { 107: 0,0}, @@ -22025,608 +21498,1377 @@ 107: 10,15}, 107: 11,16}, 107: } -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -90: done -90: hits2: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 -90: processing2 -90: launch2 :0 -90: launch2 :1 -90: launch2 :2 -90: launch2 :3 -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -111: [17:55:19] done -70: Atropisomers- 1 hits 3 misses -70: Final results: -70: Found atropisomers in TestMultInSDF.sdf - 1 hits 4 misses -111: [17:55:19] ------------------------------------- -111: [17:55:19] Test Lipinski parameters. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 80/236 Test #70: testAtropisomers ....................... Passed 0.41 sec -test 122 - Start 122: testGETAWAY - -122: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testGETAWAY -122: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -122: Test timeout computed to be: 1500 -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -68: Test -68: -68: marvin03.mrv -68: -68: Test -68: -68: Cubane.mrv -68: -68: Test -68: -68: FalseAtropisomer.mrv -68: -68: Test -68: -68: AtropEnhancedStereo.mrv -68: -68: Test -68: -68: AtropManyChirals.mrv -68: -68: Test -68: -68: AtropManyChiralsEnhanced.mrv -68: -68: Test -68: -68: AtropManyChiralsEnhanced2.mrv -68: -68: Test -68: -68: AtropManyChiralsEnhanced3.mrv -68: -68: Test -68: -68: AtropManyChiralsEnhanced4.mrv -68: -68: Test -68: -68: BMS-986142_3d_chiral.mrv -68: -68: Test -68: -68: BMS-986142_3d.mrv -68: -68: Test -68: -68: BMS-986142_atrop1.mrv -68: -68: Test -68: -68: BMS-986142_atrop2.mrv -68: -68: Test -68: -68: BMS-986142_atrop3.mrv -68: -68: Test -68: -68: BMS-986142_atrop4.mrv -68: -68: Test -68: -68: BMS-986142_atrop5.mrv -68: -68: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -68: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -90: done -90: preprocessing 3 -90: hits3: 1110100011001000010011100110100011011000010101000100110010101111011100101000001111110000010100100110 -90: processing3 -90: launch3 :0 -90: launch3 :1 -90: launch3 :2 -90: launch3 :3 -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -93: [17:55:19] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) -93: [17:55:19] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) -93: -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -65: [17:55:19] Warning: stereochemistry around double bond may be incorrect in depiction. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -68: Test -68: -68: BMS-986142_atrop6.mrv -68: -68: Test -68: -68: BMS-986142_atrop7.mrv -68: -68: Test -68: -68: BMS-986142_atrop8.mrv -68: -68: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -68: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -93: [17:55:19] Mismatched potential rlabels: 1 unmapped reactant dummy atom rlabels,0 unmappped product dummy atom rlabels -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -93: ------------- -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -93: CCOc1ccccc1 -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: Randomness seeded to: 3951529458 -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -68: Test -68: -68: BMS-986142_atropBad2.mrv -68: -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -68: [17:55:19] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -68: Test -68: -68: JDQ443_3d.mrv -68: -68: Test -68: -68: JDQ443_atrop1.mrv -68: -68: Test -68: -68: JDQ443_atrop2.mrv -68: -68: Test -68: -68: JDQ443_atrop3.mrv -68: -68: Test -68: -68: JDQ443_atropBad1.mrv -68: -68: [17:55:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -68: Test -68: -68: RP-6306_atrop1.mrv -68: -68: Test -68: -68: RP-6306_atrop2.mrv -68: -68: Test -68: -68: RP-6306_atrop3.mrv -68: -68: Test -68: -68: RP-6306_atrop4.mrv -68: -68: Test -68: -68: RP-6306_atrop5.mrv -68: -68: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -68: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -68: Test -68: -68: RP-6306_atropBad1.mrv -68: -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -68: [17:55:19] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -67: ..............[17:55:19] SMILES Parse Error: syntax error while parsing: invalidsmiles -67: [17:55:19] SMILES Parse Error: check for mistakes around position 1: -67: [17:55:19] invalidsmiles -67: [17:55:19] ^ -67: [17:55:19] SMILES Parse Error: Failed parsing SMILES 'invalidsmiles' for input: 'invalidsmiles' -68: Test -68: -68: RP-6306_atropBad2.mrv -68: -68: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -68: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -68: [17:55:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -102: Randomness seeded to: 229640199 -102: =============================================================================== -102: All tests passed (93 assertions in 13 test cases) -102: -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. - 81/236 Test #102: tautomerQueryTestCatch ................. Passed 0.22 sec +60: Test +60: +60: RP-6306_3d.cxsmi +60: +60: Test +60: +60: Sotorasib_atrop1.cxsmi +60: +60: Test +60: +60: Sotorasib_atrop2.cxsmi +60: +60: Test +60: +60: Sotorasib_atrop3.cxsmi +60: +60: Test +60: +60: Sotorasib_atrop4.cxsmi +60: +60: Test +60: +60: Sotorasib_atrop5.cxsmi +60: +60: [14:17:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [14:17:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [14:17:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [14:17:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [14:17:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [14:17:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +111: [14:17:38] done +111: [14:17:38] ------------------------------------- +111: [14:17:38] Test Lipinski parameters. + 83/236 Test #93: testReaction ........................... Passed 0.68 sec test 123 Start 123: testAUTOCORR3D 123: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testAUTOCORR3D 123: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 123: Test timeout computed to be: 1500 -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [17:55:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +60: [14:17:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [14:17:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +120: [14:17:38] ------------------------------------- +120: [14:17:38] Basic PMI tests. +60: [14:17:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [14:17:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +89: Randomness seeded to: 1540656776 +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +115: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +60: Test +60: +60: Sotorasib_atropBad1.cxsmi +60: +60: [14:17:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +60: [14:17:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +60: [14:17:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +115: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +60: [14:17:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +115: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +60: [14:17:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +115: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +60: Test +60: +60: Sotorasib_atropBad2.cxsmi +60: +60: [14:17:38] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +60: [14:17:38] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +115: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +60: [14:17:38] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +60: [14:17:38] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +115: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +60: [14:17:38] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +115: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +115: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +90: done +90: [14:17:38] done +90: [14:17:38] ------------------------------------- +90: [14:17:38] Test GitHub issue 15 +90: [14:17:38] done +90: [14:17:38] ------------------------------------- +90: [14:17:38] Test GitHub issue 409 +90: [14:17:38] done +90: [14:17:38] ------------------------------------- +90: [14:17:38] Test chiral matching +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +115: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +90: [14:17:38] done +90: [14:17:38] ------------------------------------- +90: [14:17:38] Test GitHub issue 688: partially specified chiral substructure queries don't work properly +90: [14:17:38] done +90: [14:17:38] ------------------------------------- +90: [14:17:38] Test dative-bond matching +90: [14:17:38] done +90: [14:17:38] ------------------------------------- +90: [14:17:38] Test cis/trans matching +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +90: [14:17:38] done +90: [14:17:38] ------------------------------------- +90: [14:17:38] Test cis/trans matching part 2 +90: [14:17:38] done +90: [14:17:38] ------------------------------------- +90: [14:17:38] Testing Github #1389: Substructure matching with chirality failure when query is built from SMARTS +90: [14:17:38] done +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +115: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +89: [14:17:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +115: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +90: [14:17:38] ------------------------------------- +90: [14:17:38] Testing matching E/Z against Cis/Trans stereo bonds +115: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +90: [14:17:38] +90: +90: **** +115: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +90: Pre-condition Violation +90: matches must not be empty +90: Violation occurred on line 44 in file ./Code/GraphMol/Substruct/SubstructUtils.cpp +90: Failed Expression: !matches.empty() +90: ---------- +90: Stacktrace: +90: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +90: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +90: 2# RDKit::detail::ScoreMatchesByDegreeOfCoreSubstitution::ScoreMatchesByDegreeOfCoreSubstitution(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > > const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +90: 3# RDKit::getMostSubstitutedCoreMatch(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > > const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +90: 4# 0x000055C815ADB38A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: 5# 0x000055C815ACBBF1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: 6# 0x00007F4418833CA8 in /lib/x86_64-linux-gnu/libc.so.6 +90: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +90: 8# 0x000055C815ACBD31 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: ---------- +90: **** +90: +90: [14:17:38] +90: +90: **** +90: Pre-condition Violation +90: matches must not be empty +90: Violation occurred on line 44 in file ./Code/GraphMol/Substruct/SubstructUtils.cpp +90: Failed Expression: !matches.empty() +90: ---------- +90: Stacktrace: +90: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +90: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +90: 2# RDKit::detail::ScoreMatchesByDegreeOfCoreSubstitution::ScoreMatchesByDegreeOfCoreSubstitution(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > > const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +90: 3# RDKit::sortMatchesByDegreeOfCoreSubstitution(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > > const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +90: 4# 0x000055C815AC6420 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: 5# 0x000055C815ACBBF1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: 6# 0x00007F4418833CA8 in /lib/x86_64-linux-gnu/libc.so.6 +90: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +90: 8# 0x000055C815ACBD31 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: ---------- +90: **** +90: +90: [14:17:38] ------------------------------------- +90: [14:17:38] Test substructure matching with a pathological case for symmetric SSSR +90: [14:17:38] ------------------------------------- +90: [14:17:38] Test isAtomTerminalRGroupOrQueryHydrogen +115: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. + 84/236 Test #90: testSubstructMatch ..................... Passed 0.93 sec +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: 100 -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -68: Test -68: -68: RP-6306_3d.mrv -68: -68: Test -68: -68: Sotorasib_atrop1.mrv -68: -68: Test -68: -68: Sotorasib_atrop2.mrv -68: -68: Test -68: -68: Sotorasib_atrop3.mrv -68: -68: Test -68: -68: Sotorasib_atrop4.mrv -68: -68: Test -68: -68: Sotorasib_atrop5.mrv -68: -68: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -68: [17:55:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -68: Test -68: -68: Sotorasib_atropBad1.mrv -68: -68: [17:55:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -68: Test -68: -68: Sotorasib_atropBad2.mrv -68: -68: [17:55:19] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -91: Randomness seeded to: 3829339582 +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +67: ..............[14:17:39] SMILES Parse Error: syntax error while parsing: invalidsmiles +67: [14:17:39] SMILES Parse Error: check for mistakes around position 1: +67: [14:17:39] invalidsmiles +67: [14:17:39] ^ +67: [14:17:39] SMILES Parse Error: Failed parsing SMILES 'invalidsmiles' for input: 'invalidsmiles' +91: Randomness seeded to: 2375423867 91: =============================================================================== 91: All tests passed (242 assertions in 12 test cases) 91: -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -99: .[17:55:19] reactant 0 has no mapped atoms. -99: [17:55:19] product 0 has no mapped atoms. -99: [17:55:19] reactant 0 has no mapped atoms. -99: [17:55:19] product 0 has no mapped atoms. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 82/236 Test #91: substructTestCatch ..................... Passed 0.32 sec -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +116: [14:17:39] done +116: [14:17:39] ------------------------------------- +116: [14:17:39] PBF edge cases. test 124 Start 124: testCoulombMat -124: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testCoulombMat -124: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -124: Test timeout computed to be: 1500 -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -99: .[17:55:19] reactant 0 has no mapped atoms. -99: [17:55:19] reactant 1 has no mapped atoms. -99: [17:55:19] product 0 has no mapped atoms. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -99: [17:55:19] reactant 0 has no mapped atoms. -99: [17:55:19] reactant 1 has no mapped atoms. -99: [17:55:19] product 0 has no mapped atoms. -99: [17:55:19] reactant 0 has no mapped atoms. -99: [17:55:19] reactant 1 has no mapped atoms. -99: [17:55:19] product 0 has no mapped atoms. -99: [17:55:19] reactant 0 has no mapped atoms. -99: [17:55:19] reactant 1 has no mapped atoms. -99: [17:55:19] product 0 has no mapped atoms. -99: [17:55:19] reactant 0 has no mapped atoms. -99: [17:55:19] reactant 1 has no mapped atoms. -99: [17:55:19] product 0 has no mapped atoms. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -99: [17:55:19] reactant 0 has no mapped atoms. -99: [17:55:19] reactant 1 has no mapped atoms. -99: [17:55:19] product 0 has no mapped atoms. -99: [17:55:19] reactant 0 has no mapped atoms. -99: [17:55:19] reactant 1 has no mapped atoms. -99: [17:55:19] product 0 has no mapped atoms. -99: [17:55:19] reactant 0 has no mapped atoms. -99: [17:55:19] reactant 1 has no mapped atoms. -99: [17:55:19] product 0 has no mapped atoms. -99: [17:55:19] reactant 0 has no mapped atoms. -99: [17:55:19] reactant 1 has no mapped atoms. -99: [17:55:19] product 0 has no mapped atoms. -99: [17:55:19] reactant 0 has no mapped atoms. -99: [17:55:19] reactant 1 has no mapped atoms. -99: [17:55:19] product 0 has no mapped atoms. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -99: [17:55:19] reactant 0 has no mapped atoms. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -99: [17:55:19] reactant 1 has no mapped atoms. -99: [17:55:19] product 0 has no mapped atoms. -99: [17:55:19] reactant 0 has no mapped atoms. -99: [17:55:19] reactant 1 has no mapped atoms. -99: [17:55:19] product 0 has no mapped atoms. -99: [17:55:19] reactant 0 has no mapped atoms. -99: [17:55:19] reactant 1 has no mapped atoms. -99: [17:55:19] product 0 has no mapped atoms. -99: [17:55:19] reactant 0 has no mapped atoms. -99: [17:55:19] reactant 1 has no mapped atoms. -99: [17:55:19] product 0 has no mapped atoms. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +124: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testCoulombMat +124: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +124: Test timeout computed to be: 1500 + 85/236 Test #91: substructTestCatch ..................... Passed 1.09 sec +test 125 + Start 125: descriptorsTestCatch + +125: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/descriptorsTestCatch +125: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +125: Test timeout computed to be: 1500 +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: ..... +103: ---------------------------------------------------------------------- +103: Ran 5 tests in 0.218s +103: +103: OK +124: ===================== Testing CoulombMat ======================= +124: CM test 1 mat Done +111: [14:17:39] done +111: [14:17:39] ------------------------------------- +111: [14:17:39] Test VSA descriptors. +111: [14:17:39] done +111: [14:17:39] ------------------------------------- +111: [14:17:39] Test molecular formula calculation. +111: [14:17:39] done +111: [14:17:39] ------------------------------------- +111: [14:17:39] Test Issue 3415534. +111: [14:17:39] done +111: [14:17:39] ------------------------------------- +111: [14:17:39] Test Issue3433771: Bad definition for Crippen atom type O11. +111: [14:17:39] done +111: [14:17:39] ------------------------------------- +111: [14:17:39] Test multithreading +111: reading molecules +116: [14:17:39] done + 86/236 Test #124: testCoulombMat ......................... Passed 0.10 sec +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +60: Test +60: +60: Sotorasib_3d.cxsmi +60: +60: Test +60: +60: ZM374979_atrop1.cxsmi +60: +60: Test +60: +60: ZM374979_atrop2.cxsmi +60: +60: Test +60: +60: ZM374979_atrop3.cxsmi +60: +60: Test +60: +60: ZM374979_atrop4.cxsmi +60: +60: Test +60: +60: ZM374979_atropBad1.cxsmi +60: +60: [14:17:39] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +test 126 + Start 126: pyMolDescriptors + +126: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/Wrap/testMolDescriptors.py" +126: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/Wrap +126: Test timeout computed to be: 1500 +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +60: [14:17:39] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +60: [14:17:39] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +60: [14:17:39] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +60: [14:17:39] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +108: :488: RuntimeWarning: to-Python converter for boost::shared_ptr already registered; second conversion method ignored. + 87/236 Test #116: testPBF ................................ Passed 0.67 sec +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +test 127 + Start 127: pyMolDescriptors3D + +127: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/Wrap/test3D.py" +127: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/Wrap +127: Test timeout computed to be: 1500 +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +111: processing +111: launch :0 +111: launch :1 +111: launch :2 +111: launch :3 + 88/236 Test #103: pyTautomerQuery ........................ Passed 0.94 sec +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +test 128 + Start 128: testFingerprints + +128: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/testFingerprints +128: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints +128: Test timeout computed to be: 1500 + 89/236 Test #107: filterCatalogTest ...................... Passed 0.90 sec +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +test 129 + Start 129: testMHFPFingerprint + +129: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/testMHFPFingerprint +129: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints +129: Test timeout computed to be: 1500 +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +35: [14:17:39] Maximum BFS search size exceeded. +35: This is likely due to a highly symmetric fused ring system. +121: =>start test WHIM +121: [14:17:39] test on : 365 molecules done + 90/236 Test #121: testWHIM ............................... Passed 0.64 sec +test 130 + Start 130: testFingerprintGenerators + +130: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/testFingerprintGenerators +130: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints +130: Test timeout computed to be: 1500 +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +128: +128: +128: +128: +128: +128: +128: +128: +128: +128: ------------------- +128: +128: +128: +128: +128: +128: +128: +128: +128: +128: ------------------- +128: Atoms: +128: 0 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 +128: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 2 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 +128: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 4 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 +128: 5 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 +128: 6 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 +128: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 9 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 +128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 +128: Bonds: +128: 0 0->1 order: 1 conj?: 1 +128: 1 1->2 order: a conj?: 1 aromatic?: 1 +128: 2 2->3 order: a conj?: 1 aromatic?: 1 +128: 3 3->4 order: a conj?: 1 aromatic?: 1 +128: 4 4->5 order: a conj?: 1 aromatic?: 1 +128: 5 5->6 order: a conj?: 1 aromatic?: 1 +128: 6 6->7 order: a conj?: 1 aromatic?: 1 +128: 7 7->8 order: a conj?: 1 aromatic?: 1 +128: 8 8->9 order: 1 conj?: 1 +128: 9 8->10 order: a conj?: 1 aromatic?: 1 +128: 10 10->1 order: a conj?: 1 aromatic?: 1 +128: 11 7->3 order: a conj?: 1 aromatic?: 1 +128: +128: +128: +128: +128: +128: +128: +128: +128: +128: ------------------- +128: SMI: Oc1cc2[nH]cnc2c(O)n1 +128: Atoms: +128: 0 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 +128: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 2 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 +128: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 4 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 +128: 5 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 +128: 6 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 +128: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 9 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 +128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 +128: Bonds: +128: 0 0->1 order: 1 conj?: 1 +128: 1 1->2 order: a conj?: 1 aromatic?: 1 +128: 2 2->3 order: a conj?: 1 aromatic?: 1 +128: 3 3->4 order: a conj?: 1 aromatic?: 1 +128: 4 4->5 order: a conj?: 1 aromatic?: 1 +128: 5 5->6 order: a conj?: 1 aromatic?: 1 +128: 6 6->7 order: a conj?: 1 aromatic?: 1 +128: 7 7->8 order: a conj?: 1 aromatic?: 1 +128: 8 8->9 order: 1 conj?: 1 +128: 9 8->10 order: a conj?: 1 aromatic?: 1 +128: 10 10->1 order: a conj?: 1 aromatic?: 1 +128: 11 7->3 order: a conj?: 1 aromatic?: 1 +128: +128: +128: +128: +128: +128: +128: +128: +128: +128: ------------------- +128: +128: SMI: c1(O)cc2[nH]cnc2c(O)n1 +128: Atoms: +128: 0 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 1 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 +128: 2 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 +128: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 4 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 +128: 5 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 +128: 6 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 +128: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 9 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 +128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 +128: Bonds: +128: 0 0->1 order: 1 conj?: 1 +128: 1 0->2 order: a conj?: 1 aromatic?: 1 +128: 2 2->3 order: a conj?: 1 aromatic?: 1 +128: 3 3->4 order: a conj?: 1 aromatic?: 1 +128: 4 4->5 order: a conj?: 1 aromatic?: 1 +128: 5 5->6 order: a conj?: 1 aromatic?: 1 +128: 6 6->7 order: a conj?: 1 aromatic?: 1 +128: 7 7->8 order: a conj?: 1 aromatic?: 1 +128: 8 8->9 order: 1 conj?: 1 +128: 9 8->10 order: a conj?: 1 aromatic?: 1 +128: 10 10->0 order: a conj?: 1 aromatic?: 1 +128: 11 7->3 order: a conj?: 1 aromatic?: 1 +128: +128: +128: +128: +128: +128: +128: +128: +128: +128: ------------------- +128: +128: SMI: c1c(O)nc(O)c2c1[nH]cn2 +128: Atoms: +128: 0 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 +128: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 2 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 +128: 3 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 +128: 4 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 5 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 +128: 6 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 8 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 +128: 9 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 +128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 +128: Bonds: +128: 0 0->1 order: a conj?: 1 aromatic?: 1 +128: 1 1->2 order: 1 conj?: 1 +128: 2 1->3 order: a conj?: 1 aromatic?: 1 +128: 3 3->4 order: a conj?: 1 aromatic?: 1 +128: 4 4->5 order: 1 conj?: 1 +128: 5 4->6 order: a conj?: 1 aromatic?: 1 +128: 6 6->7 order: a conj?: 1 aromatic?: 1 +128: 7 7->8 order: a conj?: 1 aromatic?: 1 +128: 8 8->9 order: a conj?: 1 aromatic?: 1 +128: 9 9->10 order: a conj?: 1 aromatic?: 1 +128: 10 7->0 order: a conj?: 1 aromatic?: 1 +128: 11 10->6 order: a conj?: 1 aromatic?: 1 +128: +128: +128: +128: +128: +128: +128: +128: +128: +128: ------------------- +128: +128: SMI: c12cc(O)nc(O)c1nc[nH]2 +128: Atoms: +128: 0 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 1 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 +128: 2 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 3 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 +128: 4 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 +128: 5 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 6 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 +128: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 8 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 +128: 9 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 +128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 +128: Bonds: +128: 0 0->1 order: a conj?: 1 aromatic?: 1 +128: 1 1->2 order: a conj?: 1 aromatic?: 1 +128: 2 2->3 order: 1 conj?: 1 +128: 3 2->4 order: a conj?: 1 aromatic?: 1 +128: 4 4->5 order: a conj?: 1 aromatic?: 1 +128: 5 5->6 order: 1 conj?: 1 +128: 6 5->7 order: a conj?: 1 aromatic?: 1 +128: 7 7->8 order: a conj?: 1 aromatic?: 1 +128: 8 8->9 order: a conj?: 1 aromatic?: 1 +128: 9 9->10 order: a conj?: 1 aromatic?: 1 +128: 10 7->0 order: a conj?: 1 aromatic?: 1 +128: 11 10->0 order: a conj?: 1 aromatic?: 1 +128: +128: +128: +128: +128: +128: +128: +128: +128: +128: ------------------- +128: +128: SMI: [nH]1c2cc(O)nc(O)c2nc1 +128: Atoms: +128: 0 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 +128: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 2 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 +128: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 4 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 +128: 5 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 +128: 6 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 7 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 +128: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 9 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 +128: 10 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 +128: Bonds: +128: 0 0->1 order: a conj?: 1 aromatic?: 1 +128: 1 1->2 order: a conj?: 1 aromatic?: 1 +128: 2 2->3 order: a conj?: 1 aromatic?: 1 +128: 3 3->4 order: 1 conj?: 1 +128: 4 3->5 order: a conj?: 1 aromatic?: 1 +128: 5 5->6 order: a conj?: 1 aromatic?: 1 +128: 6 6->7 order: 1 conj?: 1 +128: 7 6->8 order: a conj?: 1 aromatic?: 1 +128: 8 8->9 order: a conj?: 1 aromatic?: 1 +128: 9 9->10 order: a conj?: 1 aromatic?: 1 +128: 10 10->0 order: a conj?: 1 aromatic?: 1 +128: 11 8->1 order: a conj?: 1 aromatic?: 1 +128: +128: +128: +128: +128: +128: +128: +128: +128: +128: ------------------- +128: +128: SMI: c1[nH]c2cc(O)nc(O)c2n1 +128: Atoms: +128: 0 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 +128: 1 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 +128: 2 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 3 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 +128: 4 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 5 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 +128: 6 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 +128: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 8 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 +128: 9 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 +128: Bonds: +128: 0 0->1 order: a conj?: 1 aromatic?: 1 +128: 1 1->2 order: a conj?: 1 aromatic?: 1 +128: 2 2->3 order: a conj?: 1 aromatic?: 1 +128: 3 3->4 order: a conj?: 1 aromatic?: 1 +128: 4 4->5 order: 1 conj?: 1 +128: 5 4->6 order: a conj?: 1 aromatic?: 1 +128: 6 6->7 order: a conj?: 1 aromatic?: 1 +128: 7 7->8 order: 1 conj?: 1 +128: 8 7->9 order: a conj?: 1 aromatic?: 1 +128: 9 9->10 order: a conj?: 1 aromatic?: 1 +128: 10 10->0 order: a conj?: 1 aromatic?: 1 +128: 11 9->2 order: a conj?: 1 aromatic?: 1 +128: +128: +128: +128: +128: +128: +128: +128: +128: +128: ------------------- +128: +128: SMI: n1c[nH]c2cc(O)nc(O)c21 +128: Atoms: +128: 0 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 +128: 1 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 +128: 2 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 +128: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 4 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 +128: 5 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 6 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +117: =>start test rdf custom +117: [14:17:39] test on : 365 molecules done +128: 7 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 +128: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 9 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 +128: 10 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: Bonds: +128: 0 0->1 order: a conj?: 1 aromatic?: 1 +128: 1 1->2 order: a conj?: 1 aromatic?: 1 +128: 2 2->3 order: a conj?: 1 aromatic?: 1 +128: 3 3->4 order: a conj?: 1 aromatic?: 1 +128: 4 4->5 order: a conj?: 1 aromatic?: 1 +128: 5 5->6 order: 1 conj?: 1 +128: 6 5->7 order: a conj?: 1 aromatic?: 1 +128: 7 7->8 order: a conj?: 1 aromatic?: 1 +128: 8 8->9 order: 1 conj?: 1 +128: 9 8->10 order: a conj?: 1 aromatic?: 1 +128: 10 10->0 order: a conj?: 1 aromatic?: 1 +128: 11 10->3 order: a conj?: 1 aromatic?: 1 +128: +128: +128: +128: +128: +128: +128: +128: +128: +128: ------------------- +128: +128: SMI: c12c(cc(O)nc1O)[nH]cn2 +128: Atoms: +128: 0 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 2 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 +128: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 4 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 +128: 5 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 +128: 6 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 7 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 +128: 8 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 +128: 9 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 +128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 +128: Bonds: +128: 0 0->1 order: a conj?: 1 aromatic?: 1 +128: 1 1->2 order: a conj?: 1 aromatic?: 1 +128: 2 2->3 order: a conj?: 1 aromatic?: 1 +128: 3 3->4 order: 1 conj?: 1 +128: 4 3->5 order: a conj?: 1 aromatic?: 1 +128: 5 5->6 order: a conj?: 1 aromatic?: 1 +128: 6 6->7 order: 1 conj?: 1 +128: 7 1->8 order: a conj?: 1 aromatic?: 1 +128: 8 8->9 order: a conj?: 1 aromatic?: 1 +128: 9 9->10 order: a conj?: 1 aromatic?: 1 +128: 10 6->0 order: a conj?: 1 aromatic?: 1 +128: 11 10->0 order: a conj?: 1 aromatic?: 1 +128: +128: +128: +128: +128: +128: +128: +128: +128: +128: ------------------- +128: +129: [14:17:39] ------------------------------------- +129: [14:17:39] Test MHFP fingerprint encoder initialization +128: SMI: c1(O)c2c(cc(O)n1)[nH]cn2 +128: Atoms: +128: 0 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 1 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 +128: 2 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 4 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 +128: 5 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 6 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 +128: 7 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 +128: 8 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 +128: 9 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 +128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 +128: Bonds: +128: 0 0->1 order: 1 conj?: 1 +128: 1 0->2 order: a conj?: 1 aromatic?: 1 +128: 2 2->3 order: a conj?: 1 aromatic?: 1 +128: 3 3->4 order: a conj?: 1 aromatic?: 1 +128: 4 4->5 order: a conj?: 1 aromatic?: 1 +128: 5 5->6 order: 1 conj?: 1 +128: 6 5->7 order: a conj?: 1 aromatic?: 1 +128: 7 3->8 order: a conj?: 1 aromatic?: 1 +128: 8 8->9 order: a conj?: 1 aromatic?: 1 +128: 9 9->10 order: a conj?: 1 aromatic?: 1 +128: 10 7->0 order: a conj?: 1 aromatic?: 1 +128: 11 10->2 order: a conj?: 1 aromatic?: 1 +128: +128: +128: +128: +128: +128: +128: +128: +128: +128: ------------------- +128: +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +128: SMI: Oc1c2c(cc(O)n1)[nH]cn2 +128: Atoms: +128: 0 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 +128: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 2 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 4 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 +128: 5 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 6 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 +128: 7 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 +128: 8 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 +128: 9 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 +128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 +128: Bonds: +128: 0 0->1 order: 1 conj?: 1 +128: 1 1->2 order: a conj?: 1 aromatic?: 1 +128: 2 2->3 order: a conj?: 1 aromatic?: 1 +128: 3 3->4 order: a conj?: 1 aromatic?: 1 +128: 4 4->5 order: a conj?: 1 aromatic?: 1 +128: 5 5->6 order: 1 conj?: 1 +128: 6 5->7 order: a conj?: 1 aromatic?: 1 +128: 7 3->8 order: a conj?: 1 aromatic?: 1 +128: 8 8->9 order: a conj?: 1 aromatic?: 1 +128: 9 9->10 order: a conj?: 1 aromatic?: 1 +128: 10 7->1 order: a conj?: 1 aromatic?: 1 +128: 11 10->2 order: a conj?: 1 aromatic?: 1 +128: +128: +128: +128: +128: +128: +128: +128: +128: +128: ------------------- +128: +128: SMI: n1c(O)cc2[nH]cnc2c1O +128: Atoms: +128: 0 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 +128: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 2 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 +128: 3 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 +128: 4 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 5 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 +128: 6 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 +128: 7 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 +128: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 9 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 10 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 +128: Bonds: +128: 0 0->1 order: a conj?: 1 aromatic?: 1 +128: 1 1->2 order: 1 conj?: 1 +128: 2 1->3 order: a conj?: 1 aromatic?: 1 +128: 3 3->4 order: a conj?: 1 aromatic?: 1 +128: 4 4->5 order: a conj?: 1 aromatic?: 1 +128: 5 5->6 order: a conj?: 1 aromatic?: 1 +128: 6 6->7 order: a conj?: 1 aromatic?: 1 +128: 7 7->8 order: a conj?: 1 aromatic?: 1 +128: 8 8->9 order: a conj?: 1 aromatic?: 1 +128: 9 9->10 order: 1 conj?: 1 +128: 10 9->0 order: a conj?: 1 aromatic?: 1 +128: 11 8->4 order: a conj?: 1 aromatic?: 1 +128: +128: +128: +128: +128: +128: +128: +128: +128: +128: ------------------- +128: +128: +128: +128: +128: +128: +128: +128: +128: +128: +128: ------------------- +98: [14:17:39] == testCartesianProduct +110: ......... +110: ---------------------------------------------------------------------- +110: Ran 9 tests in 0.185s +110: +110: OK +128: +128: +128: +128: +128: +128: +128: +128: +128: +128: ------------------- +128: +128: [14:17:39] ------------------------------------- +128: [14:17:39] Test Morgan Fingerprints. +130: [14:17:39] ------------------------------------- +130: [14:17:39] Test atom-pair fp generator +60: Test +60: +60: Mrtx1719_3d.cxsmi +60: +60: Test +60: +60: Mrtx1719_atrop1.cxsmi +60: +60: Test +60: +60: Mrtx1719_atrop2.cxsmi +60: +60: Test +60: +60: Mrtx1719_atrop3.cxsmi +60: +60: Test +60: +60: Mrtx1719_atrop4.cxsmi +60: +60: Test +60: +60: Mrtx1719_atropBad1.cxsmi +60: +60: [14:17:39] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +128: [14:17:39] done +128: [14:17:39] ------------------------------------- +128: [14:17:39] Test Morgan Fingerprints using fromAtoms argument. +128: [14:17:39] done +128: [14:17:39] ------------------------------------- +128: [14:17:39] Test Morgan Fingerprints as bit vects. +128: [14:17:39] done +128: [14:17:39] ------------------------------------- +128: [14:17:39] Test Morgan Fingerprints with feature invariants. +128: [14:17:39] done +128: [14:17:39] ------------------------------------- +128: [14:17:39] Test additional Morgan fingerprints options. +128: [14:17:39] done +128: [14:17:39] ------------------------------------- +128: [14:17:39] Test Atom Codes. +128: [14:17:39] done +128: [14:17:39] ------------------------------------- +128: [14:17:39] Test Atom Pairs. +128: [14:17:39] DEPRECATION WARNING: please use AtomPairGenerator +128: [14:17:39] DEPRECATION WARNING: please use AtomPairGenerator +128: [14:17:39] done +128: [14:17:39] ------------------------------------- +128: [14:17:39] Test Atom Pairs part 2. +128: [14:17:39] DEPRECATION WARNING: please use AtomPairGenerator +128: [14:17:39] DEPRECATION WARNING: please use AtomPairGenerator +128: [14:17:39] done +128: [14:17:39] ------------------------------------- +128: [14:17:39] Test Topological Torsions. +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] done +128: [14:17:39] ------------------------------------- +128: [14:17:39] Test Bulk Topological Torsions. +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +60: [14:17:39] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +60: [14:17:39] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +60: [14:17:39] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +60: [14:17:39] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +123: =>start test autocorr3D +123: [14:17:39] test on : 365 molecules done +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +99: .[14:17:39] reactant 0 has no mapped atoms. +99: [14:17:39] product 0 has no mapped atoms. +99: [14:17:39] reactant 0 has no mapped atoms. +99: [14:17:39] product 0 has no mapped atoms. +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +35: F/C=C/Cl +35: [H]/C(F)=C(/[H])Cl +35: F/C=C/Cl +35: F/C=C/Cl +35: C/C(F)=C(/C)Cl +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [14:17:39] done +130: [14:17:39] ------------------------------------- +130: [14:17:39] Test atom-pair fp generator with different arguments +130: [14:17:39] done +130: [14:17:39] ------------------------------------- +130: [14:17:39] Test compatibility between atom pair implementation for FingerprintGenerator and old atom pairs implementation +130: [14:17:39] DEPRECATION WARNING: please use AtomPairGenerator +130: [14:17:39] DEPRECATION WARNING: please use AtomPairGenerator +130: [14:17:39] DEPRECATION WARNING: please use AtomPairGenerator +130: [14:17:39] DEPRECATION WARNING: please use AtomPairGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +98: .[14:17:39] == testEnumerateLibrary +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator + 91/236 Test #123: testAUTOCORR3D ......................... Passed 0.72 sec +test 131 + Start 131: fpTestCatch + +131: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/fpTestCatch +131: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints +131: Test timeout computed to be: 1500 +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +99: .[14:17:39] reactant 0 has no mapped atoms. +99: [14:17:39] reactant 1 has no mapped atoms. +99: [14:17:39] product 0 has no mapped atoms. +99: [14:17:39] reactant 0 has no mapped atoms. +99: [14:17:39] reactant 1 has no mapped atoms. +99: [14:17:39] product 0 has no mapped atoms. +99: [14:17:39] reactant 0 has no mapped atoms. +99: [14:17:39] reactant 1 has no mapped atoms. +99: [14:17:39] product 0 has no mapped atoms. +99: [14:17:39] reactant 0 has no mapped atoms. +99: [14:17:39] reactant 1 has no mapped atoms. +99: [14:17:39] product 0 has no mapped atoms. +130: [14:17:39] DEPRECATION WARNING: please use AtomPairGenerator +130: [14:17:39] DEPRECATION WARNING: please use AtomPairGenerator +130: [14:17:39] DEPRECATION WARNING: please use AtomPairGenerator +130: [14:17:39] DEPRECATION WARNING: please use AtomPairGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +97: ...[14:17:39] +97: +97: **** +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +129: [14:17:39] done +129: [14:17:39] ------------------------------------- +129: [14:17:39] Test MHFP shingling creation +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +99: [14:17:39] reactant 0 has no mapped atoms. +99: [14:17:39] reactant 1 has no mapped atoms. +99: [14:17:39] product 0 has no mapped atoms. +99: [14:17:39] reactant 0 has no mapped atoms. +99: [14:17:39] reactant 1 has no mapped atoms. +99: [14:17:39] product 0 has no mapped atoms. +99: [14:17:39] reactant 0 has no mapped atoms. +99: [14:17:39] reactant 1 has no mapped atoms. +99: [14:17:39] product 0 has no mapped atoms. +99: [14:17:39] reactant 0 has no mapped atoms. +99: [14:17:39] reactant 1 has no mapped atoms. +99: [14:17:39] product 0 has no mapped atoms. +99: [14:17:39] reactant 0 has no mapped atoms. +99: [14:17:39] reactant 1 has no mapped atoms. +99: [14:17:39] product 0 has no mapped atoms. +99: [14:17:39] reactant 0 has no mapped atoms. +99: [14:17:39] reactant 1 has no mapped atoms. +99: [14:17:39] product 0 has no mapped atoms. +99: [14:17:39] reactant 0 has no mapped atoms. +99: [14:17:39] reactant 1 has no mapped atoms. +99: [14:17:39] product 0 has no mapped atoms. +99: [14:17:39] reactant 0 has no mapped atoms. +99: [14:17:39] reactant 1 has no mapped atoms. +99: [14:17:39] product 0 has no mapped atoms. +99: [14:17:39] reactant 0 has no mapped atoms. +99: [14:17:39] reactant 1 has no mapped atoms. +99: [14:17:39] product 0 has no mapped atoms. +99: [14:17:39] reactant 0 has no mapped atoms. +99: [14:17:39] reactant 1 has no mapped atoms. +99: [14:17:39] product 0 has no mapped atoms. 99: () 99: ******************************************** 99: $RXN @@ -22990,359 +23232,25 @@ 99: 1 2 1 0 99: M ISO 2 1 1 2 2 99: M END -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -99: [17:55:19] reactant 0 has no mapped atoms. -99: [17:55:19] reactant 1 has no mapped atoms. -99: [17:55:19] product 0 has no mapped atoms. -99: [17:55:19] Could not find RLabel mapping for atom: 0 in template: 1 -99: [17:55:19] reactant 1 has no mapped atoms. -99: [17:55:19] reactant 1 has no mapped atoms. -99: [17:55:19] reactant 1 has no mapped atoms. -99: .. -99: ---------------------------------------------------------------------- -99: Ran 4 tests in 0.028s -99: -99: OK -99: -99: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -99: $RXN -99: -99: RDKit -99: -99: 2 1 -99: $MOL -99: -99: RDKit 2D -99: -99: 2 1 0 1 0 0 0 0 0 0999 V2000 -99: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 -99: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 -99: 1 2 1 0 -99: M RGP 1 2 1 -99: V 1 halogen.bromine.aromatic -99: V 2 [*:1] -99: M STY 1 1 DAT -99: M SAL 1 1 1 -99: M SED 1 [#35&$([Br&$(Br-&!@c)])] -99: M END -99: $MOL -99: -99: RDKit 2D -99: -99: 4 3 0 1 0 0 0 0 0 0999 V2000 -99: 3.4375 -7.7917 0.0000 R3 0 0 0 0 0 0 0 0 0 0 0 0 -99: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 -99: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -99: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -99: 2 3 1 0 -99: 1 2 1 0 -99: 2 4 1 0 -99: M ISO 1 1 3 -99: V 2 boronicacid -99: M STY 1 1 DAT -99: M SAL 1 1 2 -99: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] -99: M END -99: $MOL -99: -99: RDKit 2D -99: -99: 2 1 0 0 0 0 0 0 0 0999 V2000 -99: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 -99: 11.9811 -6.9292 0.0000 R2 0 0 0 0 0 0 0 0 0 0 0 0 -99: 1 2 1 0 -99: M ISO 1 2 2 -99: M RGP 1 1 1 -99: V 1 [*:1] -99: M END -99: -99: $RXN Failed -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -111: [17:55:19] done -111: [17:55:19] ------------------------------------- -111: [17:55:19] Test VSA descriptors. -108: :488: RuntimeWarning: to-Python converter for boost::shared_ptr already registered; second conversion method ignored. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -111: [17:55:19] done -111: [17:55:19] ------------------------------------- -111: [17:55:19] Test molecular formula calculation. -111: [17:55:19] done -111: [17:55:19] ------------------------------------- -111: [17:55:19] Test Issue 3415534. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -111: [17:55:19] done -111: [17:55:19] ------------------------------------- -98: [17:55:19] == testCartesianProduct -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -68: Test -68: -68: Sotorasib_3d.mrv -68: -68: Test -68: -68: ZM374979_atrop1.mrv -68: -68: Test -68: -68: ZM374979_atrop2.mrv -68: -68: Test -68: -68: ZM374979_atrop3.mrv -68: -68: Test -68: -68: ZM374979_atropBad1.mrv -68: -68: [17:55:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -124: ===================== Testing CoulombMat ======================= -111: [17:55:19] Test Issue3433771: Bad definition for Crippen atom type O11. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -111: [17:55:19] done -111: [17:55:19] ------------------------------------- -111: [17:55:19] Test multithreading -111: reading molecules -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -30: ......[17:55:19] Molecule does not have explicit Hs. Consider calling AddHs() -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -75: [17:55:19] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -75: 0.40201265 0.40201265 -75: -0.13299436 -0.13299436 -75: 1.00000017 1.00000017 -75: 0.8762226 0.8762226 -75: 0.9973909 0.9973909 -75: 1.00000003 1.00000003 -75: 0.36613799 0.36613799 -75: 2.1107185 2.1107185 -75: 0.99999982 0.99999982 -75: 2.48696157 2.48696157 -75: 1.00479935 1.00479935 -75: 0.99999999 0.99999999 -75: 3.03311841 3.03311841 -75: 2.23739955 2.23739955 -75: 1.0000001 1.0000001 -75: 3.00772337 3.00772337 -75: 0.37399294 0.37399294 -75: 2.07713325 2.07713325 -75: 3.0077234 3.0077234 -75: 0.37399312 0.37399312 -75: -0.07713336 -0.07713336 -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -98: .[17:55:19] == testEnumerateLibrary -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -75: [17:55:19] bond with order 0 found on line 11. This is not part of the MDL specification. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -75: [17:55:19] bond with order 0 found on line 16. This is not part of the MDL specification. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -124: CM test 1 mat Done -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 83/236 Test #124: testCoulombMat ......................... Passed 0.04 sec -test 125 - Start 125: descriptorsTestCatch - -125: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/descriptorsTestCatch -125: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -125: Test timeout computed to be: 1500 -90: done -90: [17:55:19] done -90: [17:55:19] ------------------------------------- -90: [17:55:19] Test GitHub issue 15 -90: [17:55:19] done -90: [17:55:19] ------------------------------------- -90: [17:55:19] Test GitHub issue 409 -90: [17:55:19] done -90: [17:55:19] ------------------------------------- -90: [17:55:19] Test chiral matching -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -98: /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py:266: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/testData/enumeration.pickle'> -98: open(os.path.join(self.dataDir, "enumeration.pickle"), 'rb').read()) -98: ResourceWarning: Enable tracemalloc to get the object allocation traceback -68: Test -68: -68: mrtx1719_3d.mrv -68: -68: Test -68: -68: mrtx1719_atrop1.mrv -68: -68: Test -68: -68: mrtx1719_atrop2.mrv -68: -68: Test -68: -68: mrtx1719_atrop3.mrv -68: -68: Test -68: -68: mrtx1719_atropBad1.mrv -68: -68: [17:55:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -103: ..... -103: ---------------------------------------------------------------------- -103: Ran 5 tests in 0.042s -103: -103: OK - 84/236 Test #65: testDepictor ........................... Passed 0.61 sec -test 126 - Start 126: pyMolDescriptors - -126: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/Wrap/testMolDescriptors.py" -126: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/Wrap -126: Test timeout computed to be: 1500 -104: Finished -104: ----------------------- -104: testRootedSubgraphs -104: Finished -104: ----------------------- -104: testRootedPaths -104: Finished -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -90: [17:55:19] done -90: [17:55:19] ------------------------------------- -90: [17:55:19] Test GitHub issue 688: partially specified chiral substructure queries don't work properly -90: [17:55:19] done -90: [17:55:19] ------------------------------------- -90: [17:55:19] Test dative-bond matching -90: [17:55:19] done -90: [17:55:19] ------------------------------------- -90: [17:55:19] Test cis/trans matching -90: [17:55:19] done -90: [17:55:19] ------------------------------------- -90: [17:55:19] Test cis/trans matching part 2 -90: [17:55:19] done -90: [17:55:19] ------------------------------------- -90: [17:55:19] Testing Github #1389: Substructure matching with chirality failure when query is built from SMARTS - 85/236 Test #99: pyChemReactionSanitize ................. Passed 0.33 sec - 86/236 Test #104: testSubgraphs1 ......................... Passed 0.31 sec -90: [17:55:19] done -test 127 - Start 127: pyMolDescriptors3D - -127: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/Wrap/test3D.py" -127: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/Wrap -127: Test timeout computed to be: 1500 -test 128 - Start 128: testFingerprints - -128: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/testFingerprints -128: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints -128: Test timeout computed to be: 1500 -90: [17:55:20] ------------------------------------- -90: [17:55:20] Testing matching E/Z against Cis/Trans stereo bonds -111: processing -111: launch :0 -111: launch :1 -111: launch :2 -111: launch :3 -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 87/236 Test #75: testMolWriter .......................... Passed 0.58 sec -test 129 - Start 129: testMHFPFingerprint - -129: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/testMHFPFingerprint -129: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints -129: Test timeout computed to be: 1500 -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -90: [17:55:20] -90: -90: **** -90: Pre-condition Violation -90: matches must not be empty -90: Violation occurred on line 44 in file ./Code/GraphMol/Substruct/SubstructUtils.cpp -90: Failed Expression: !matches.empty() -90: ---------- -90: Stacktrace: -90: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -90: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -90: 2# RDKit::detail::ScoreMatchesByDegreeOfCoreSubstitution::ScoreMatchesByDegreeOfCoreSubstitution(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > > const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -90: 3# RDKit::getMostSubstitutedCoreMatch(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > > const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -90: 4# 0x0000564B1BF6438A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -90: 5# 0x0000564B1BF54BF1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -90: 6# 0x00007F2071633CA8 in /lib/x86_64-linux-gnu/libc.so.6 -90: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -90: 8# 0x0000564B1BF54D31 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -90: ---------- -90: **** -90: -90: [17:55:20] -90: -90: **** -90: Pre-condition Violation -90: matches must not be empty -90: Violation occurred on line 44 in file ./Code/GraphMol/Substruct/SubstructUtils.cpp -90: Failed Expression: !matches.empty() -90: ---------- -90: Stacktrace: -90: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -90: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -90: 2# RDKit::detail::ScoreMatchesByDegreeOfCoreSubstitution::ScoreMatchesByDegreeOfCoreSubstitution(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > > const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -90: 3# RDKit::sortMatchesByDegreeOfCoreSubstitution(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > > const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -90: 4# 0x0000564B1BF4F420 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -90: 5# 0x0000564B1BF54BF1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -90: 6# 0x00007F2071633CA8 in /lib/x86_64-linux-gnu/libc.so.6 -90: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -90: 8# 0x0000564B1BF54D31 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -90: ---------- -90: **** -90: -90: [17:55:20] ------------------------------------- -90: [17:55:20] Test substructure matching with a pathological case for symmetric SSSR -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -116: [17:55:20] done -116: [17:55:20] ------------------------------------- -116: [17:55:20] PBF edge cases. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -116: [17:55:20] done -90: [17:55:20] ------------------------------------- -90: [17:55:20] Test isAtomTerminalRGroupOrQueryHydrogen -97: ...[17:55:20] -97: -97: **** - 88/236 Test #90: testSubstructMatch ..................... Passed 0.40 sec - 89/236 Test #107: filterCatalogTest ...................... Passed 0.32 sec - 90/236 Test #116: testPBF ................................ Passed 0.28 sec -67: ..... -67: ---------------------------------------------------------------------- -67: Ran 19 tests in 0.402s -67: -67: OK -test 130 - Start 130: testFingerprintGenerators - -130: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/testFingerprintGenerators -130: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints -130: Test timeout computed to be: 1500 -test 131 - Start 131: fpTestCatch - -131: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/fpTestCatch -131: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints -131: Test timeout computed to be: 1500 -test 132 - Start 132: fpGenTestCatch - -132: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/fpGenTestCatch -132: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints -132: Test timeout computed to be: 1500 +99: [14:17:39] reactant 0 has no mapped atoms. +99: [14:17:39] reactant 1 has no mapped atoms. +99: [14:17:39] product 0 has no mapped atoms. +99: [14:17:39] Could not find RLabel mapping for atom: 0 in template: 1 +99: [14:17:39] reactant 1 has no mapped atoms. +99: [14:17:39] reactant 1 has no mapped atoms. +99: [14:17:39] reactant 1 has no mapped atoms. +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +35: [14:17:39] ----------------------- +35: Testing isRingFused +130: [14:17:39] DEPRECATION WARNING: please use AtomPairGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator 97: Pre-condition Violation 97: getNumImplicitHs() called without preceding call to calcImplicitValence() 97: Violation occurred on line 301 in file ./Code/GraphMol/Atom.cpp @@ -23374,7 +23282,7 @@ 97: 22# _object* RDKit::RunReactants(RDKit::ChemicalReaction*, boost::python::tuple, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 97: 23# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 97: 24# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -97: 25# 0x00007FC746CC362C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +97: 25# 0x00007F6A1DB8B62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 97: 26# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 97: 27# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 97: 28# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so @@ -23385,17 +23293,17 @@ 97: 33# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 97: 34# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 97: 35# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -97: 36# 0x00007FC7449B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -97: 37# 0x00007FC7449B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -97: 38# 0x00007FC7449B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -97: 39# 0x00007FC7449B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -97: 40# 0x00007FC7449B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +97: 36# 0x00007F6A1B7B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +97: 37# 0x00007F6A1B7B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +97: 38# 0x00007F6A1B7B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +97: 39# 0x00007F6A1B7B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +97: 40# 0x00007F6A1B7B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 97: 41# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 97: 42# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 97: 43# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 97: 44# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 97: 45# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -97: 46# 0x00007FC746CC03C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +97: 46# 0x00007F6A1DB883C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 97: 47# _PyObject_MakeTpCall in /usr/bin/python3 97: 48# _PyEval_EvalFrameDefault in /usr/bin/python3 97: 49# 0x00000000005CD3C9 in /usr/bin/python3 @@ -23427,15 +23335,171 @@ 97: 75# 0x00000000006B921E in /usr/bin/python3 97: 76# Py_RunMain in /usr/bin/python3 97: 77# Py_BytesMain in /usr/bin/python3 -97: 78# 0x00007FC7476C8CA8 in /lib/x86_64-linux-gnu/libc.so.6 +97: 78# 0x00007F6A1E590CA8 in /lib/x86_64-linux-gnu/libc.so.6 97: 79# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 97: 80# _start in /usr/bin/python3 97: ---------- 97: **** 97: -97: [17:55:20] +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: 200 +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +98: /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py:266: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/testData/enumeration.pickle'> +98: open(os.path.join(self.dataDir, "enumeration.pickle"), 'rb').read()) +98: ResourceWarning: Enable tracemalloc to get the object allocation traceback + 92/236 Test #35: graphmolMolOpsTest ..................... Passed 2.60 sec +test 132 + Start 132: fpGenTestCatch + +132: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/fpGenTestCatch +132: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints +132: Test timeout computed to be: 1500 +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +99: .. +99: ---------------------------------------------------------------------- +99: Ran 4 tests in 0.135s +99: +99: OK +99: +99: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> +99: $RXN +99: +99: RDKit +99: +99: 2 1 +99: $MOL +99: +99: RDKit 2D +99: +99: 2 1 0 1 0 0 0 0 0 0999 V2000 +99: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 +99: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 +99: 1 2 1 0 +99: M RGP 1 2 1 +99: V 1 halogen.bromine.aromatic +99: V 2 [*:1] +99: M STY 1 1 DAT +99: M SAL 1 1 1 +99: M SED 1 [#35&$([Br&$(Br-&!@c)])] +99: M END +99: $MOL +99: +99: RDKit 2D +99: +99: 4 3 0 1 0 0 0 0 0 0999 V2000 +99: 3.4375 -7.7917 0.0000 R3 0 0 0 0 0 0 0 0 0 0 0 0 +99: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 +99: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +99: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +99: 2 3 1 0 +99: 1 2 1 0 +99: 2 4 1 0 +99: M ISO 1 1 3 +99: V 2 boronicacid +99: M STY 1 1 DAT +99: M SAL 1 1 2 +99: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] +99: M END +99: $MOL +99: +99: RDKit 2D +99: +99: 2 1 0 0 0 0 0 0 0 0999 V2000 +99: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 +99: 11.9811 -6.9292 0.0000 R2 0 0 0 0 0 0 0 0 0 0 0 0 +99: 1 2 1 0 +99: M ISO 1 2 2 +99: M RGP 1 1 1 +99: V 1 [*:1] +99: M END +99: +99: $RXN Failed +97: [14:17:39] 97: 97: **** +130: [14:17:39] DEPRECATION WARNING: please use AtomPairGenerator +130: [14:17:39] done +130: [14:17:39] ------------------------------------- +130: [14:17:39] Test atom-pair additional output +130: [14:17:39] done +130: [14:17:39] ------------------------------------- +130: [14:17:39] Test Folded Atom Pairs. +130: [14:17:39] done +130: [14:17:39] ------------------------------------- +130: [14:17:39] Test Rooted Atom Pairs. +130: [14:17:39] done +130: [14:17:39] ------------------------------------- +130: [14:17:39] Test ignoring atoms in Atom Pairs. +130: [14:17:39] done +130: [14:17:39] ------------------------------------- +130: [14:17:39] Test Atom Pairs including info about chirality. +130: [14:17:39] done +130: [14:17:39] ------------------------------------- +130: [14:17:39] Test Morgan Fingerprints. +130: [14:17:39] done +130: [14:17:39] ------------------------------------- +130: [14:17:39] Test morgan fp generator +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +125: Randomness seeded to: 1580277255 +125: Warning: Atom Count for residue GLU5A does not match expected count + 93/236 Test #110: pyFragCatalog .......................... Passed 1.07 sec +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +test 133 + Start 133: pyTestGenerator + +133: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/Wrap/testGenerators.py" +133: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap +133: Test timeout computed to be: 1500 +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +125: Warning: Atom Count for residue ASN39A does not match expected count +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 97: Pre-condition Violation 97: getNumImplicitHs() called without preceding call to calcImplicitValence() 97: Violation occurred on line 301 in file ./Code/GraphMol/Atom.cpp @@ -23467,7 +23531,7 @@ 97: 22# _object* RDKit::RunReactants(RDKit::ChemicalReaction*, boost::python::tuple, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 97: 23# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 97: 24# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -97: 25# 0x00007FC746CC362C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +97: 25# 0x00007F6A1DB8B62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 97: 26# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 97: 27# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 97: 28# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so @@ -23478,17 +23542,17 @@ 97: 33# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 97: 34# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 97: 35# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -97: 36# 0x00007FC7449B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -97: 37# 0x00007FC7449B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -97: 38# 0x00007FC7449B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -97: 39# 0x00007FC7449B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -97: 40# 0x00007FC7449B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +97: 36# 0x00007F6A1B7B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +97: 37# 0x00007F6A1B7B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +97: 38# 0x00007F6A1B7B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +97: 39# 0x00007F6A1B7B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +97: 40# 0x00007F6A1B7B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 97: 41# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 97: 42# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 97: 43# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 97: 44# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 97: 45# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -97: 46# 0x00007FC746CC03C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +97: 46# 0x00007F6A1DB883C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 97: 47# _PyObject_MakeTpCall in /usr/bin/python3 97: 48# _PyEval_EvalFrameDefault in /usr/bin/python3 97: 49# 0x00000000005CD3C9 in /usr/bin/python3 @@ -23520,1682 +23584,924 @@ 97: 75# 0x00000000006B921E in /usr/bin/python3 97: 76# Py_RunMain in /usr/bin/python3 97: 77# Py_BytesMain in /usr/bin/python3 -97: 78# 0x00007FC7476C8CA8 in /lib/x86_64-linux-gnu/libc.so.6 +97: 78# 0x00007F6A1E590CA8 in /lib/x86_64-linux-gnu/libc.so.6 97: 79# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 97: 80# _start in /usr/bin/python3 97: ---------- 97: **** 97: -129: [17:55:20] ------------------------------------- -129: [17:55:20] Test MHFP fingerprint encoder initialization -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -93: [17:55:20] reactant 0 has no mapped atoms. -93: [17:55:20] product 0 has no mapped atoms. -93: [17:55:20] WARNING: neither stereo atoms nor CIP codes found for double bond. Stereochemistry info will not be propagated to product. -98: ..[17:55:20] == testRGroupState - 91/236 Test #103: pyTautomerQuery ........................ Passed 0.36 sec -97: .........[17:55:20] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -97: [17:55:20] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -97: [17:55:20] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -97: [17:55:20] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -97: .[17:55:20] product atom-mapping number 1 found multiple times. -97: [17:55:20] product atom-mapping number 1 found multiple times. -110: ......... -110: ---------------------------------------------------------------------- -110: Ran 9 tests in 0.069s -110: -110: OK -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -98: .[17:55:20] == testRandomEnumerateAllBBsLibrary +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +125: Warning: Atom Count for residue GLU53A does not match expected count +125: Warning: Atom Count for residue ARG64A does not match expected count +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [14:17:39] done +130: [14:17:39] ------------------------------------- +130: [14:17:39] Test Morgan Fingerprints using fromAtoms argument. +130: [14:17:39] done +130: [14:17:39] ------------------------------------- +130: [14:17:39] Test Morgan Fingerprints as bit vects. +130: [14:17:39] done +130: [14:17:39] ------------------------------------- +130: [14:17:39] Test Morgan Fingerprints with feature invariants. +130: [14:17:39] done +130: [14:17:39] ------------------------------------- +130: [14:17:39] Test additional Morgan fingerprints options. +130: [14:17:39] done +130: [14:17:39] ------------------------------------- +130: [14:17:39] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints +130: [14:17:39] done +130: [14:17:39] ------------------------------------- +130: [14:17:39] Single atoms setting radius 1 bits in Morgan fingerprints +130: [14:17:39] done +130: [14:17:39] ------------------------------------- +130: [14:17:39] Test different invariant generator combinations +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +125: Warning: Atom Count for residue LYS80A does not match expected count +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +130: [14:17:39] done +130: [14:17:39] ------------------------------------- +130: [14:17:39] Test invariant overriding +130: [14:17:39] done +130: [14:17:39] ------------------------------------- +130: [14:17:39] Test RDKit fp generator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] done +128: [14:17:39] ------------------------------------- +128: [14:17:39] Test Hashed Atom Pairs. +128: [14:17:39] DEPRECATION WARNING: please use AtomPairGenerator +128: [14:17:39] DEPRECATION WARNING: please use AtomPairGenerator +128: [14:17:39] DEPRECATION WARNING: please use AtomPairGenerator +128: [14:17:39] DEPRECATION WARNING: please use AtomPairGenerator +128: [14:17:39] DEPRECATION WARNING: please use AtomPairGenerator +128: [14:17:39] DEPRECATION WARNING: please use AtomPairGenerator +128: [14:17:39] done +128: [14:17:39] ------------------------------------- +128: [14:17:39] Test Hashed torsions. +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] done +128: [14:17:39] ------------------------------------- +128: [14:17:39] Test Rooted Atom Pairs. +128: [14:17:39] DEPRECATION WARNING: please use AtomPairGenerator +128: [14:17:39] DEPRECATION WARNING: please use AtomPairGenerator +128: [14:17:39] done +128: [14:17:39] ------------------------------------- +128: [14:17:39] Test ignoring atoms in Atom Pairs. +128: [14:17:39] DEPRECATION WARNING: please use AtomPairGenerator +128: [14:17:39] DEPRECATION WARNING: please use AtomPairGenerator +128: [14:17:39] DEPRECATION WARNING: please use AtomPairGenerator +128: [14:17:39] DEPRECATION WARNING: please use AtomPairGenerator +128: [14:17:39] DEPRECATION WARNING: please use AtomPairGenerator +128: [14:17:39] done +128: [14:17:39] ------------------------------------- +128: [14:17:39] Test Rooted Topological Torsions. +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] done +128: [14:17:39] ------------------------------------- +128: [14:17:39] Test ignoring atoms in Topological Torsions. +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] done +128: [14:17:39] ------------------------------------- +128: [14:17:39] Test atom info from morgan fingerprints. +128: [14:17:39] done +128: [14:17:39] ------------------------------------- +128: [14:17:39] Test atom info from morgan fingerprints including Info Redundant Environments. +131: Randomness seeded to: 140437991 +131: =============================================================================== +131: All tests passed (188 assertions in 16 test cases) +131: +128: [14:17:39] done +128: [14:17:39] ------------------------------------- +128: [14:17:39] ------------------------------------- +128: [14:17:39] DEPRECATION WARNING: please use AtomPairGenerator +128: [14:17:39] DEPRECATION WARNING: please use AtomPairGenerator +128: [14:17:39] DEPRECATION WARNING: please use AtomPairGenerator +128: [14:17:39] DEPRECATION WARNING: please use AtomPairGenerator +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. + 94/236 Test #131: fpTestCatch ............................ Passed 0.12 sec +128: [14:17:39] DEPRECATION WARNING: please use AtomPairGenerator +128: [14:17:39] DEPRECATION WARNING: please use AtomPairGenerator +128: [14:17:39] DEPRECATION WARNING: please use AtomPairGenerator +128: [14:17:39] DEPRECATION WARNING: please use AtomPairGenerator +test 134 + Start 134: pyTestMHFP + +134: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/Wrap/testMHFP.py" +134: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap +134: Test timeout computed to be: 1500 +128: [14:17:39] DEPRECATION WARNING: please use AtomPairGenerator +128: [14:17:39] DEPRECATION WARNING: please use AtomPairGenerator +128: [14:17:39] DEPRECATION WARNING: please use AtomPairGenerator +128: [14:17:39] DEPRECATION WARNING: please use AtomPairGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] ------------------------------------- +128: [14:17:39] ------------------------------------- +128: [14:17:39] ------------------------------------- +128: [14:17:39] ------------------------------------- +128: [14:17:39] Test Atom Pairs including info about chirality. +128: [14:17:39] DEPRECATION WARNING: please use AtomPairGenerator +128: [14:17:39] DEPRECATION WARNING: please use AtomPairGenerator +128: [14:17:39] DEPRECATION WARNING: please use AtomPairGenerator +128: [14:17:39] DEPRECATION WARNING: please use AtomPairGenerator +128: [14:17:39] DEPRECATION WARNING: please use AtomPairGenerator +128: [14:17:39] DEPRECATION WARNING: please use AtomPairGenerator +128: [14:17:39] DEPRECATION WARNING: please use AtomPairGenerator +128: [14:17:39] DEPRECATION WARNING: please use AtomPairGenerator +128: [14:17:39] DEPRECATION WARNING: please use AtomPairGenerator +128: [14:17:39] DEPRECATION WARNING: please use AtomPairGenerator +128: [14:17:39] DEPRECATION WARNING: please use AtomPairGenerator +128: [14:17:39] DEPRECATION WARNING: please use AtomPairGenerator +128: [14:17:39] done +128: [14:17:39] ------------------------------------- +128: [14:17:39] Test Topological Torsions including info about chirality. +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] done +128: [14:17:39] ------------------------------------- +128: [14:17:39] Test GitHub Issue 25: fingerprint backwards compatibility. +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:39] DEPRECATION WARNING: please use AtomPairGenerator +128: [14:17:39] DEPRECATION WARNING: please use AtomPairGenerator +128: [14:17:39] done +128: [14:17:39] ------------------------------------- +128: [14:17:39] Test GitHub Issue 151: PatternFingerprint problems +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +125: Warning: Atom Count for residue GLU150A does not match expected count +125: Warning: Atom Count for residue ASN157A does not match expected count +129: [14:17:39] done +129: [14:17:39] ------------------------------------- +129: [14:17:39] Test MHFP hashing of string and uint arrays +129: [14:17:39] done +129: [14:17:39] ------------------------------------- +129: [14:17:39] Test SECFP fingerprint functionality +97: .........[14:17:39] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +97: [14:17:39] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +97: [14:17:39] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +97: [14:17:39] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +97: .[14:17:39] product atom-mapping number 1 found multiple times. +97: [14:17:39] product atom-mapping number 1 found multiple times. +67: ..... +67: ---------------------------------------------------------------------- +67: Ran 19 tests in 1.466s +67: +67: OK +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: Finished +104: ----------------------- +104: testRootedSubgraphs +104: Finished +104: ----------------------- +104: testRootedPaths +104: Finished + 95/236 Test #104: testSubgraphs1 ......................... Passed 1.30 sec +test 135 + Start 135: testPartialCharges + +135: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/testPartialCharges +135: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges +135: Test timeout computed to be: 1500 +70: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +128: [14:17:39] done +128: [14:17:39] ------------------------------------- +128: [14:17:39] Test 3D atom pairs. +128: [14:17:39] DEPRECATION WARNING: please use AtomPairGenerator +128: [14:17:39] DEPRECATION WARNING: please use AtomPairGenerator +128: [14:17:39] DEPRECATION WARNING: please use AtomPairGenerator +128: [14:17:39] DEPRECATION WARNING: please use AtomPairGenerator +128: [14:17:39] DEPRECATION WARNING: please use AtomPairGenerator +128: [14:17:39] done +128: [14:17:39] ------------------------------------- +128: [14:17:39] Test GitHub Issue 195: GenMACCSKeys() raises an exception with an empty molecule +128: [14:17:39] done +128: [14:17:39] ------------------------------------- +128: [14:17:39] Test multithreading with the pattern FP +128: reading molecules +129: [14:17:39] done +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. + 96/236 Test #129: testMHFPFingerprint .................... Passed 0.34 sec +test 136 + Start 136: pyPartialCharges + +136: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/PartialCharges/Wrap/testPartialCharges.py" +136: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/Wrap +136: Test timeout computed to be: 1500 +97: ................[14:17:39] mapped atoms in the reactants were not mapped in the products. +97: unmapped numbers are: 3 +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +97: [14:17:39] mapped atoms in the reactants were not mapped in the products. +97: unmapped numbers are: 3 +97: .:488: RuntimeWarning: to-Python converter for boost::shared_ptr already registered; second conversion method ignored. +97: [14:17:39] mapped atoms in the reactants were not mapped in the products. +97: unmapped numbers are: 3 +70: Atropisomers- 1 hits 3 misses +70: Final results: +70: Found atropisomers in TestMultInSDF.sdf - 1 hits 4 misses + 97/236 Test #70: testAtropisomers ....................... Passed 2.04 sec +test 137 + Start 137: testMolTransforms + +137: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/testMolTransforms +137: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms +137: Test timeout computed to be: 1500 +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +97: ..[14:17:39] reactant 2 has no mapped atoms. +97: [14:17:39] reactant 2 has no mapped atoms. +97: [14:17:39] product 1 has no mapped atoms. + 98/236 Test #135: testPartialCharges ..................... Passed 0.09 sec +test 138 + Start 138: molTransformsTestCatch + +138: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/molTransformsTestCatch +138: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms +138: Test timeout computed to be: 1500 +128: pass 1 +128: launch :0 +128: launch :1 +128: launch :2 +128: launch :3 +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +97: ........[14:17:39] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])Q +97: [14:17:39] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])Q' for input: '[C:1](=[O:2])Q' +97: [14:17:39] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])[N:3]Q +97: [14:17:39] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])[N:3]Q' for input: '[C:1](=[O:2])[N:3]Q' +98: ..[14:17:39] == testRGroupState + 99/236 Test #99: pyChemReactionSanitize ................. Passed 1.51 sec +test 139 + Start 139: pyMolTransforms + +139: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolTransforms/Wrap/testMolTransforms.py" +139: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap +139: Test timeout computed to be: 1500 +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +97: .[14:17:39] reactant atom-mapping number 1 found multiple times. +97: [14:17:39] product atom-mapping number 2 not found in reactants. +97: [14:17:39] mapped atoms in the reactants were not mapped in the products. +97: unmapped numbers are: 4 +97: [14:17:39] product atom-mapping number 5 not found in reactants. +92: Randomness seeded to: 3970920246 +92: =============================================================================== +92: All tests passed (11480 assertions in 38 test cases) +92: +100/236 Test #92: testGenericGroups ...................... Passed 1.72 sec +test 140 + Start 140: forceFieldHelpersCatch + +140: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/forceFieldHelpersCatch +140: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers +140: Test timeout computed to be: 1500 +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +98: .[14:17:39] == testRandomEnumerateAllBBsLibrary 98: ** [1, 1] 98: ** [0, 2] 98: ** [1, 0] -130: [17:55:20] ------------------------------------- -130: [17:55:20] Test atom-pair fp generator +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +132: Randomness seeded to: 1497378717 +132: =============================================================================== +132: All tests passed (2737 assertions in 7 test cases) +132: +101/236 Test #132: fpGenTestCatch ......................... Passed 0.28 sec +test 141 + Start 141: testMMFFForceFieldHelpers + +141: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpers +141: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF +141: Test timeout computed to be: 1500 +138: Randomness seeded to: 779828891 +138: =============================================================================== +138: All tests passed (4 assertions in 1 test case) +138: +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +102/236 Test #138: molTransformsTestCatch ................. Passed 0.10 sec +test 142 + Start 142: testMMFFForceFieldHelpersMultiThread + +142: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpersMultiThread +142: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF +142: Test timeout computed to be: 1500 +98: .[14:17:39] == testRandomEnumerateLibrary +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +89: [14:17:39] Explicit valence for atom # 9 N, 5, is greater than permitted +137: *********************************************************** +137: Testing MolTransforms +137: --------------------------------- +137: test1Canonicalization +137: +137: --------------------------------- +137: testGetSetBondLength +137: +137: --------------------------------- +137: testGetSetAngle +137: +137: --------------------------------- +137: testGetSetDihedral +137: +137: --------------------------------- +137: testGetSetDihedralThroughTripleBond +137: +137: --------------------------------- +137: testGithub1262: PMI descriptors incorrect +137: +137: --------------------------------- +137: testGithub1908: CanonicalizeMol() distorting bond lengths +137: +137: --------------------------------- +137: testGithub4302: native computeCanonicalTransform() generates non-canonical coords +137: +137: --------------------------------- +137: testWeightedCentroid +137: +137: *********************************************************** +103/236 Test #67: pyDepictor ............................. Passed 2.24 sec +test 143 + Start 143: testUFFForceFieldHelpers + +143: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF/testUFFForceFieldHelpers +143: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF +143: Test timeout computed to be: 1500 +104/236 Test #137: testMolTransforms ...................... Passed 0.18 sec +test 144 + Start 144: testCrystalForceField + +144: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalForceField +144: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF +144: Test timeout computed to be: 1500 +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +141: [14:17:39] ------------------------------------- +141: [14:17:39] Test MMFF atom types. +98: .[14:17:39] == testRandomSample +98: .[14:17:39] == testRandomSampleAllBBs +120: [14:17:39] done +120: [14:17:39] ------------------------------------- +120: [14:17:39] More PMI/NPR tests. +142: [14:17:39] ------------------------------------- +142: [14:17:39] Test MMFF multithreading 68: Test 68: -68: FalseAtropisomer.mrv +68: badWedgeError.sdf 68: 68: Test 68: -68: AtropEnhancedStereo.mrv +68: CrossedDoubleBondWithChiralNbr2.sdf 68: 68: Test 68: -68: AtropManyChirals.mrv +68: CrossedDoubleBondWithChiralNbr.sdf 68: 68: Test 68: -68: AtropManyChiralsEnhanced.mrv +68: SimpleWiggleDoubleBond.sdf 68: 68: Test 68: -68: AtropManyChiralsEnhanced2.mrv +68: lostStereoAnd.sdf 68: 68: Test 68: -68: AtropManyChiralsEnhanced3.mrv +68: DoubleBondChain.sdf 68: 68: Test 68: -68: AtropManyChiralsEnhanced4.mrv +68: UnitsError.sdf 68: 68: Test 68: -68: BMS-986142_3d_chiral.mrv +68: StarAtom.sdf 68: 68: Test 68: -68: BMS-986142_3d.mrv +68: nonProprietary.mol 68: 68: Test 68: -68: BMS-986142_atrop1.mrv +68: ChiralTest.sdf 68: 68: Test 68: -68: BMS-986142_atrop2.mrv +68: TestBond1.mol 68: 68: Test 68: -68: BMS-986142_atrop3.mrv +68: Sgroup_MUL_ParentInMiddle.sdf 68: 68: Test 68: -68: BMS-986142_atrop4.mrv +68: BadRxn.rxn 68: 68: Test 68: -68: BMS-986142_atrop5.mrv +68: FalseChiral.mrv 68: -68: [17:55:20] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -68: [17:55:20] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -128: -128: -128: -128: -128: -128: -128: -128: -128: -128: ------------------- -128: -128: -128: -128: -128: -128: -128: -128: -128: -128: ------------------- -128: Atoms: -128: 0 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 -128: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 2 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 -128: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 4 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -128: 5 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 -128: 6 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -128: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 9 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 -128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -128: Bonds: -128: 0 0->1 order: 1 conj?: 1 -128: 1 1->2 order: a conj?: 1 aromatic?: 1 -128: 2 2->3 order: a conj?: 1 aromatic?: 1 -128: 3 3->4 order: a conj?: 1 aromatic?: 1 -128: 4 4->5 order: a conj?: 1 aromatic?: 1 -128: 5 5->6 order: a conj?: 1 aromatic?: 1 -128: 6 6->7 order: a conj?: 1 aromatic?: 1 -128: 7 7->8 order: a conj?: 1 aromatic?: 1 -128: 8 8->9 order: 1 conj?: 1 -128: 9 8->10 order: a conj?: 1 aromatic?: 1 -128: 10 10->1 order: a conj?: 1 aromatic?: 1 -128: 11 7->3 order: a conj?: 1 aromatic?: 1 -128: -128: -128: -128: -128: -128: -128: -128: -128: -128: ------------------- -128: SMI: Oc1cc2[nH]cnc2c(O)n1 -128: Atoms: -128: 0 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 -128: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 2 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 -128: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 4 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -128: 5 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 -128: 6 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -128: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 9 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 -128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -128: Bonds: -128: 0 0->1 order: 1 conj?: 1 -128: 1 1->2 order: a conj?: 1 aromatic?: 1 -128: 2 2->3 order: a conj?: 1 aromatic?: 1 -128: 3 3->4 order: a conj?: 1 aromatic?: 1 -128: 4 4->5 order: a conj?: 1 aromatic?: 1 -128: 5 5->6 order: a conj?: 1 aromatic?: 1 -128: 6 6->7 order: a conj?: 1 aromatic?: 1 -128: 7 7->8 order: a conj?: 1 aromatic?: 1 -128: 8 8->9 order: 1 conj?: 1 -128: 9 8->10 order: a conj?: 1 aromatic?: 1 -128: 10 10->1 order: a conj?: 1 aromatic?: 1 -128: 11 7->3 order: a conj?: 1 aromatic?: 1 -128: -128: -128: -128: -128: -128: -128: -128: -128: -128: ------------------- -128: -128: SMI: c1(O)cc2[nH]cnc2c(O)n1 -128: Atoms: -128: 0 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 1 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 -128: 2 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 -128: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 4 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -128: 5 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 -128: 6 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -128: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 9 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 -128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -128: Bonds: -128: 0 0->1 order: 1 conj?: 1 -128: 1 0->2 order: a conj?: 1 aromatic?: 1 -128: 2 2->3 order: a conj?: 1 aromatic?: 1 -128: 3 3->4 order: a conj?: 1 aromatic?: 1 -128: 4 4->5 order: a conj?: 1 aromatic?: 1 -128: 5 5->6 order: a conj?: 1 aromatic?: 1 -128: 6 6->7 order: a conj?: 1 aromatic?: 1 -128: 7 7->8 order: a conj?: 1 aromatic?: 1 -128: 8 8->9 order: 1 conj?: 1 -128: 9 8->10 order: a conj?: 1 aromatic?: 1 -128: 10 10->0 order: a conj?: 1 aromatic?: 1 -128: 11 7->3 order: a conj?: 1 aromatic?: 1 -128: -128: -128: -128: -128: -128: -128: -128: -128: -128: ------------------- -128: -128: SMI: c1c(O)nc(O)c2c1[nH]cn2 -128: Atoms: -128: 0 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 -128: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 2 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 -128: 3 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -128: 4 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 5 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 -128: 6 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 8 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -128: 9 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 -128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -128: Bonds: -128: 0 0->1 order: a conj?: 1 aromatic?: 1 -128: 1 1->2 order: 1 conj?: 1 -128: 2 1->3 order: a conj?: 1 aromatic?: 1 -128: 3 3->4 order: a conj?: 1 aromatic?: 1 -128: 4 4->5 order: 1 conj?: 1 -128: 5 4->6 order: a conj?: 1 aromatic?: 1 -128: 6 6->7 order: a conj?: 1 aromatic?: 1 -128: 7 7->8 order: a conj?: 1 aromatic?: 1 -128: 8 8->9 order: a conj?: 1 aromatic?: 1 -128: 9 9->10 order: a conj?: 1 aromatic?: 1 -128: 10 7->0 order: a conj?: 1 aromatic?: 1 -128: 11 10->6 order: a conj?: 1 aromatic?: 1 -128: -128: -128: -128: -128: -128: -128: -128: -128: -128: ------------------- -128: -128: SMI: c12cc(O)nc(O)c1nc[nH]2 -128: Atoms: -128: 0 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 1 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 -128: 2 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 3 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 -128: 4 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -128: 5 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 6 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 -128: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 8 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -128: 9 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 -128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -128: Bonds: -128: 0 0->1 order: a conj?: 1 aromatic?: 1 -128: 1 1->2 order: a conj?: 1 aromatic?: 1 -128: 2 2->3 order: 1 conj?: 1 -128: 3 2->4 order: a conj?: 1 aromatic?: 1 -128: 4 4->5 order: a conj?: 1 aromatic?: 1 -128: 5 5->6 order: 1 conj?: 1 -128: 6 5->7 order: a conj?: 1 aromatic?: 1 -128: 7 7->8 order: a conj?: 1 aromatic?: 1 -128: 8 8->9 order: a conj?: 1 aromatic?: 1 -128: 9 9->10 order: a conj?: 1 aromatic?: 1 -128: 10 7->0 order: a conj?: 1 aromatic?: 1 -128: 11 10->0 order: a conj?: 1 aromatic?: 1 -128: -128: -128: -128: -128: -128: -128: -128: -128: -128: ------------------- -128: -128: SMI: [nH]1c2cc(O)nc(O)c2nc1 -128: Atoms: -128: 0 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -128: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 2 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 -128: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 4 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 -128: 5 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -128: 6 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 7 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 -128: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 9 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -128: 10 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 -128: Bonds: -128: 0 0->1 order: a conj?: 1 aromatic?: 1 -128: 1 1->2 order: a conj?: 1 aromatic?: 1 -128: 2 2->3 order: a conj?: 1 aromatic?: 1 -128: 3 3->4 order: 1 conj?: 1 -128: 4 3->5 order: a conj?: 1 aromatic?: 1 -128: 5 5->6 order: a conj?: 1 aromatic?: 1 -128: 6 6->7 order: 1 conj?: 1 -128: 7 6->8 order: a conj?: 1 aromatic?: 1 -128: 8 8->9 order: a conj?: 1 aromatic?: 1 -128: 9 9->10 order: a conj?: 1 aromatic?: 1 -128: 10 10->0 order: a conj?: 1 aromatic?: 1 -128: 11 8->1 order: a conj?: 1 aromatic?: 1 -128: -128: -128: -128: -128: -128: -128: -128: -128: -128: ------------------- -128: -128: SMI: c1[nH]c2cc(O)nc(O)c2n1 -128: Atoms: -128: 0 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 -128: 1 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -128: 2 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 3 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 -128: 4 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 5 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 -128: 6 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -128: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 8 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 -128: 9 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -128: Bonds: -128: 0 0->1 order: a conj?: 1 aromatic?: 1 -128: 1 1->2 order: a conj?: 1 aromatic?: 1 -128: 2 2->3 order: a conj?: 1 aromatic?: 1 -128: 3 3->4 order: a conj?: 1 aromatic?: 1 -128: 4 4->5 order: 1 conj?: 1 -128: 5 4->6 order: a conj?: 1 aromatic?: 1 -128: 6 6->7 order: a conj?: 1 aromatic?: 1 -128: 7 7->8 order: 1 conj?: 1 -128: 8 7->9 order: a conj?: 1 aromatic?: 1 -128: 9 9->10 order: a conj?: 1 aromatic?: 1 -128: 10 10->0 order: a conj?: 1 aromatic?: 1 -128: 11 9->2 order: a conj?: 1 aromatic?: 1 -128: -128: -128: -128: -128: -128: -128: -128: -128: -128: ------------------- -128: -128: SMI: n1c[nH]c2cc(O)nc(O)c21 -128: Atoms: -128: 0 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -128: 1 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 -128: 2 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -128: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 4 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 -128: 5 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 6 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 -128: 7 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -128: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 9 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 -128: 10 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: Bonds: -128: 0 0->1 order: a conj?: 1 aromatic?: 1 -test 133 - Start 133: pyTestGenerator - -133: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/Wrap/testGenerators.py" -133: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap -133: Test timeout computed to be: 1500 - 92/236 Test #93: testReaction ........................... Passed 0.43 sec -97: ................[17:55:20] mapped atoms in the reactants were not mapped in the products. -97: unmapped numbers are: 3 -97: [17:55:20] mapped atoms in the reactants were not mapped in the products. -97: unmapped numbers are: 3 -97: .:488: RuntimeWarning: to-Python converter for boost::shared_ptr already registered; second conversion method ignored. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: 200 -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -98: .[17:55:20] == testRandomEnumerateLibrary -130: [17:55:20] done -130: [17:55:20] ------------------------------------- -130: [17:55:20] Test atom-pair fp generator with different arguments -130: [17:55:20] done -130: [17:55:20] ------------------------------------- -130: [17:55:20] Test compatibility between atom pair implementation for FingerprintGenerator and old atom pairs implementation -130: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -130: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -130: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -130: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -130: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -130: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -130: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -130: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -130: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator 68: Test 68: -68: BMS-986142_atrop6.mrv +68: FalseChiral.mrv 68: 68: Test 68: -68: BMS-986142_atrop7.mrv +68: Cubane.mrv 68: 68: Test 68: -68: BMS-986142_atrop8.mrv +68: NewChiralTest.mrv 68: -68: [17:55:20] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -68: [17:55:20] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 68: Test 68: -68: BMS-986142_atropBad2.mrv +68: NewChiralTest.mrv 68: -68: [17:55:20] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 -128: 1 1->2 order: a conj?: 1 aromatic?: 1 -128: 2 2->3 order: a conj?: 1 aromatic?: 1 -128: 3 3->4 order: a conj?: 1 aromatic?: 1 -128: 4 4->5 order: a conj?: 1 aromatic?: 1 -128: 5 5->6 order: 1 conj?: 1 -128: 6 5->7 order: a conj?: 1 aromatic?: 1 -128: 7 7->8 order: a conj?: 1 aromatic?: 1 -128: 8 8->9 order: 1 conj?: 1 -128: 9 8->10 order: a conj?: 1 aromatic?: 1 -128: 10 10->0 order: a conj?: 1 aromatic?: 1 -128: 11 10->3 order: a conj?: 1 aromatic?: 1 -128: -128: -128: -128: -128: -128: -128: -128: -128: -128: ------------------- -128: -128: SMI: c12c(cc(O)nc1O)[nH]cn2 -128: Atoms: -128: 0 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 2 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 -128: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 4 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 -128: 5 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -128: 6 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 7 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 -128: 8 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -128: 9 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 -128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -128: Bonds: -128: 0 0->1 order: a conj?: 1 aromatic?: 1 -128: 1 1->2 order: a conj?: 1 aromatic?: 1 -128: 2 2->3 order: a conj?: 1 aromatic?: 1 -128: 3 3->4 order: 1 conj?: 1 -128: 4 3->5 order: a conj?: 1 aromatic?: 1 -128: 5 5->6 order: a conj?: 1 aromatic?: 1 -128: 6 6->7 order: 1 conj?: 1 -128: 7 1->8 order: a conj?: 1 aromatic?: 1 -128: 8 8->9 order: a conj?: 1 aromatic?: 1 -128: 9 9->10 order: a conj?: 1 aromatic?: 1 -128: 10 6->0 order: a conj?: 1 aromatic?: 1 -128: 11 10->0 order: a conj?: 1 aromatic?: 1 -128: -128: -128: -128: -128: -128: -128: -128: -128: -128: ------------------- -128: -128: SMI: c1(O)c2c(cc(O)n1)[nH]cn2 -128: Atoms: -128: 0 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 1 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 -128: 2 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 4 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 -128: 5 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 6 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 -128: 7 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -128: 8 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -128: 9 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 -128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -128: Bonds: -128: 0 0->1 order: 1 conj?: 1 -128: 1 0->2 order: a conj?: 1 aromatic?: 1 -128: 2 2->3 order: a conj?: 1 aromatic?: 1 -128: 3 3->4 order: a conj?: 1 aromatic?: 1 -128: 4 4->5 order: a conj?: 1 aromatic?: 1 -128: 5 5->6 order: 1 conj?: 1 -128: 6 5->7 order: a conj?: 1 aromatic?: 1 -128: 7 3->8 order: a conj?: 1 aromatic?: 1 -128: 8 8->9 order: a conj?: 1 aromatic?: 1 -128: 9 9->10 order: a conj?: 1 aromatic?: 1 -128: 10 7->0 order: a conj?: 1 aromatic?: 1 -128: 11 10->2 order: a conj?: 1 aromatic?: 1 -128: -128: -128: -128: -128: -128: -128: -128: -128: -128: ------------------- -128: -128: SMI: Oc1c2c(cc(O)n1)[nH]cn2 -128: Atoms: -128: 0 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 -128: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 2 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 4 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 -128: 5 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 6 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 -128: 7 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -128: 8 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -128: 9 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 -128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -128: Bonds: -128: 0 0->1 order: 1 conj?: 1 -128: 1 1->2 order: a conj?: 1 aromatic?: 1 -128: 2 2->3 order: a conj?: 1 aromatic?: 1 -128: 3 3->4 order: a conj?: 1 aromatic?: 1 -128: 4 4->5 order: a conj?: 1 aromatic?: 1 -128: 5 5->6 order: 1 conj?: 1 -128: 6 5->7 order: a conj?: 1 aromatic?: 1 -128: 7 3->8 order: a conj?: 1 aromatic?: 1 -128: 8 8->9 order: a conj?: 1 aromatic?: 1 -128: 9 9->10 order: a conj?: 1 aromatic?: 1 -128: 10 7->1 order: a conj?: 1 aromatic?: 1 -128: 11 10->2 order: a conj?: 1 aromatic?: 1 -128: -128: -128: -128: -128: -128: -128: -128: -128: -128: ------------------- -128: -128: SMI: n1c(O)cc2[nH]cnc2c1O -128: Atoms: -128: 0 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -128: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 2 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 -128: 3 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 -128: 4 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 5 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -128: 6 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 -128: 7 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -128: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 9 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 10 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 -128: Bonds: -128: 0 0->1 order: a conj?: 1 aromatic?: 1 -128: 1 1->2 order: 1 conj?: 1 -128: 2 1->3 order: a conj?: 1 aromatic?: 1 -128: 3 3->4 order: a conj?: 1 aromatic?: 1 -128: 4 4->5 order: a conj?: 1 aromatic?: 1 -128: 5 5->6 order: a conj?: 1 aromatic?: 1 -128: 6 6->7 order: a conj?: 1 aromatic?: 1 -128: 7 7->8 order: a conj?: 1 aromatic?: 1 -128: 8 8->9 order: a conj?: 1 aromatic?: 1 -128: 9 9->10 order: 1 conj?: 1 -128: 10 9->0 order: a conj?: 1 aromatic?: 1 -128: 11 8->4 order: a conj?: 1 aromatic?: 1 -128: -128: -128: -128: -128: -128: -128: -128: -128: -128: ------------------- -128: -128: -128: -128: -128: -128: -128: -128: -128: -128: -128: ------------------- -128: -128: -128: -128: -128: -128: -128: -128: -128: -128: ------------------- -128: -128: [17:55:20] ------------------------------------- -128: [17:55:20] Test Morgan Fingerprints. -128: [17:55:20] done -128: [17:55:20] ------------------------------------- -128: [17:55:20] Test Morgan Fingerprints using fromAtoms argument. -128: [17:55:20] done -128: [17:55:20] ------------------------------------- -128: [17:55:20] Test Morgan Fingerprints as bit vects. -128: [17:55:20] done -128: [17:55:20] ------------------------------------- -128: [17:55:20] Test Morgan Fingerprints with feature invariants. -128: [17:55:20] done -128: [17:55:20] ------------------------------------- -128: [17:55:20] Test additional Morgan fingerprints options. -128: [17:55:20] done -128: [17:55:20] ------------------------------------- -128: [17:55:20] Test Atom Codes. -128: [17:55:20] done -128: [17:55:20] ------------------------------------- -128: [17:55:20] Test Atom Pairs. -128: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [17:55:20] done -128: [17:55:20] ------------------------------------- -128: [17:55:20] Test Atom Pairs part 2. -128: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [17:55:20] done -128: [17:55:20] ------------------------------------- -128: [17:55:20] Test Topological Torsions. -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -test 134 - Start 134: pyTestMHFP - -134: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/Wrap/testMHFP.py" -134: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap -134: Test timeout computed to be: 1500 -97: [17:55:20] mapped atoms in the reactants were not mapped in the products. -97: unmapped numbers are: 3 -97: ..[17:55:20] reactant 2 has no mapped atoms. -97: [17:55:20] reactant 2 has no mapped atoms. -97: [17:55:20] product 1 has no mapped atoms. -97: ........[17:55:20] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])Q -97: [17:55:20] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])Q' for input: '[C:1](=[O:2])Q' -97: [17:55:20] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])[N:3]Q -97: [17:55:20] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])[N:3]Q' for input: '[C:1](=[O:2])[N:3]Q' -97: .[17:55:20] reactant atom-mapping number 1 found multiple times. -97: [17:55:20] product atom-mapping number 2 not found in reactants. -97: [17:55:20] mapped atoms in the reactants were not mapped in the products. -97: unmapped numbers are: 4 -97: [17:55:20] product atom-mapping number 5 not found in reactants. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -98: .[17:55:20] == testRandomSample -98: .[17:55:20] == testRandomSampleAllBBs -98: .[17:55:20] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead -98: [17:55:20] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead -98: .[17:55:20] == testRemoveBadMatches -130: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -130: [17:55:20] done -130: [17:55:20] ------------------------------------- -130: [17:55:20] Test atom-pair additional output -130: [17:55:20] done -130: [17:55:20] ------------------------------------- -130: [17:55:20] Test Folded Atom Pairs. -130: [17:55:20] done -130: [17:55:20] ------------------------------------- -130: [17:55:20] Test Rooted Atom Pairs. -130: [17:55:20] done -130: [17:55:20] ------------------------------------- -130: [17:55:20] Test ignoring atoms in Atom Pairs. -130: [17:55:20] done -130: [17:55:20] ------------------------------------- -130: [17:55:20] Test Atom Pairs including info about chirality. -130: [17:55:20] done -130: [17:55:20] ------------------------------------- -130: [17:55:20] Test Morgan Fingerprints. -130: [17:55:20] done -130: [17:55:20] ------------------------------------- -130: [17:55:20] Test morgan fp generator -130: [17:55:20] done -130: [17:55:20] ------------------------------------- -130: [17:55:20] Test Morgan Fingerprints using fromAtoms argument. -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] done -128: [17:55:20] ------------------------------------- -128: [17:55:20] Test Bulk Topological Torsions. -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -129: [17:55:20] done -129: [17:55:20] ------------------------------------- -129: [17:55:20] Test MHFP shingling creation - 93/236 Test #67: pyDepictor ............................. Passed 0.68 sec -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -130: [17:55:20] done -130: [17:55:20] ------------------------------------- -130: [17:55:20] Test Morgan Fingerprints as bit vects. -130: [17:55:20] done -130: [17:55:20] ------------------------------------- -130: [17:55:20] Test Morgan Fingerprints with feature invariants. -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -120: [17:55:20] done -120: [17:55:20] ------------------------------------- -120: [17:55:20] More PMI/NPR tests. -test 135 - Start 135: testPartialCharges - -135: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/testPartialCharges -135: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges -135: Test timeout computed to be: 1500 -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -130: [17:55:20] done -130: [17:55:20] ------------------------------------- -130: [17:55:20] Test additional Morgan fingerprints options. -130: [17:55:20] done -130: [17:55:20] ------------------------------------- -130: [17:55:20] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints -130: [17:55:20] done -130: [17:55:20] ------------------------------------- -130: [17:55:20] Single atoms setting radius 1 bits in Morgan fingerprints -130: [17:55:20] done -130: [17:55:20] ------------------------------------- -130: [17:55:20] Test different invariant generator combinations -130: [17:55:20] done -130: [17:55:20] ------------------------------------- -130: [17:55:20] Test invariant overriding -130: [17:55:20] done -130: [17:55:20] ------------------------------------- -130: [17:55:20] Test RDKit fp generator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -120: [17:55:20] done -120: [17:55:20] ------------------------------------- -120: [17:55:20] Basic NPR tests. -131: Randomness seeded to: 537551968 -131: =============================================================================== -131: All tests passed (188 assertions in 16 test cases) -131: -98: .[17:55:20] == testTimings 68: Test 68: -68: JDQ443_3d.mrv +68: NewChiralTestNoChiral.mrv 68: 68: Test 68: -68: JDQ443_atrop1.mrv +68: NewChiralTestNoChiral.mrv 68: 68: Test 68: -68: JDQ443_atrop2.mrv +68: NewChiralTestAllChiral.mrv 68: 68: Test 68: -68: JDQ443_atrop3.mrv +68: NewChiralTestAllChiral.mrv 68: 68: Test 68: -68: JDQ443_atropBad1.mrv +68: DataSgroupMissingUnitsDisplayed.mrv 68: -68: [17:55:20] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 - 94/236 Test #110: pyFragCatalog .......................... Passed 0.38 sec - 95/236 Test #131: fpTestCatch ............................ Passed 0.07 sec -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -test 136 - Start 136: pyPartialCharges - -136: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/PartialCharges/Wrap/testPartialCharges.py" -136: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/Wrap -136: Test timeout computed to be: 1500 -test 137 - Start 137: testMolTransforms - -137: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/testMolTransforms -137: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms -137: Test timeout computed to be: 1500 -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -129: [17:55:20] done -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -129: [17:55:20] ------------------------------------- -129: [17:55:20] Test MHFP hashing of string and uint arrays -129: [17:55:20] done -129: [17:55:20] ------------------------------------- -129: [17:55:20] Test SECFP fingerprint functionality -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 68: Test 68: -68: RP-6306_atrop1.mrv +68: lostStereoAnd.mrv 68: 68: Test 68: -68: RP-6306_atrop2.mrv +68: DoubleBondChain.mrv 68: 68: Test 68: -68: RP-6306_atrop3.mrv +68: WigglyAndCrossed.mrv 68: 68: Test 68: -68: RP-6306_atrop4.mrv +68: BondTypes.mrv 68: 68: Test 68: -68: RP-6306_atrop5.mrv +68: EmbeddedSGroupSUP_MUL.mrv 68: -68: [17:55:20] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -68: [17:55:20] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 68: Test 68: -68: RP-6306_atropBad1.mrv +68: EmbeddedSgroupCOP_SUP.mrv 68: -68: [17:55:20] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator 68: Test 68: -68: RP-6306_atropBad2.mrv +68: EmbeddedSgroupDAT_SUP.mrv 68: -68: [17:55:20] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -68: [17:55:20] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -68: [17:55:20] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -129: [17:55:20] done -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 96/236 Test #129: testMHFPFingerprint .................... Passed 0.11 sec -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -test 138 - Start 138: molTransformsTestCatch - -138: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/molTransformsTestCatch -138: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms -138: Test timeout computed to be: 1500 -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -97: ........./build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py:745: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/testData/reaction1.no_metadata.png'> -97: png = open(fname, 'rb').read() -97: ResourceWarning: Enable tracemalloc to get the object allocation traceback -97: [17:55:20] Found a SCD/SED line with missing/empty SDT specification at line 34 -97: [17:55:20] Found a SCD/SED line with missing/empty SDT specification at line 36 -97: [17:55:20] Found a SCD/SED line with missing/empty SDT specification at line 38 -97: [17:55:20] Found a SCD/SED line with missing/empty SDT specification at line 40 -97: [17:55:20] Found a SCD/SED line with missing/empty SDT specification at line 42 -97: [17:55:20] Found a SCD/SED line with missing/empty SDT specification at line 87 -97: [17:55:20] Found a SCD/SED line with missing/empty SDT specification at line 89 -97: [17:55:20] Found a SCD/SED line with missing/empty SDT specification at line 91 -97: [17:55:20] Found a SCD/SED line with missing/empty SDT specification at line 93 -97: [17:55:20] Found a SCD/SED line with missing/empty SDT specification at line 95 -125: Randomness seeded to: 3881723152 -125: Warning: Atom Count for residue GLU5A does not match expected count -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -125: Warning: Atom Count for residue ASN39A does not match expected count -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -125: Warning: Atom Count for residue GLU53A does not match expected count -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -125: Warning: Atom Count for residue ARG64A does not match expected count -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator - 97/236 Test #135: testPartialCharges ..................... Passed 0.05 sec -97: ..[17:55:20] SMARTS Parse Error: syntax error while parsing: boromicacid -97: [17:55:20] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' -125: Warning: Atom Count for residue LYS80A does not match expected count -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -test 139 - Start 139: pyMolTransforms - -139: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolTransforms/Wrap/testMolTransforms.py" -139: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap -139: Test timeout computed to be: 1500 -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -97: [17:55:20] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide -97: [17:55:20] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' -97: [17:55:20] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride -97: [17:55:20] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' -97: [17:55:20] reaction has no reactants -97: [17:55:20] reaction has no products -97: [17:55:20] initialization failed -97: [17:55:20] reaction has no reactants -97: [17:55:20] reaction has no products -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 68: Test 68: -68: RP-6306_3d.mrv +68: EmbeddedSgroupMULTICENTER_SUP.mrv 68: 68: Test 68: -68: Sotorasib_atrop1.mrv +68: EmbeddedSgroupMUL_MUL.mrv 68: 68: Test 68: -68: Sotorasib_atrop2.mrv +68: EmbeddedSgroupMUL_MUL2.mrv 68: 68: Test 68: -68: Sotorasib_atrop3.mrv +68: EmbeddedSgroupMUL_SUP.mrv 68: 68: Test 68: -68: Sotorasib_atrop4.mrv +68: EmbeddedSgroupSRU_SUP.mrv 68: 68: Test 68: -68: Sotorasib_atrop5.mrv +68: EmbeddedSgroupSUPEXP_SUP.mrv 68: -68: [17:55:20] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -68: [17:55:20] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -97: .[17:55:20] SMARTS Parse Error: syntax error while parsing: boromicacid -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -97: [17:55:20] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' 68: Test 68: -68: Sotorasib_atropBad1.mrv +68: EmbeddedSgroupSUPEXP_SUP2.mrv 68: -68: [17:55:20] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -97: [17:55:20] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide -97: [17:55:20] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -138: Randomness seeded to: 2253073525 -138: =============================================================================== -138: All tests passed (4 assertions in 1 test case) -138: -97: [17:55:20] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride -97: [17:55:20] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' -97: [17:55:20] reaction has no reactants -97: [17:55:20] reaction has no products -97: [17:55:20] initialization failed -97: [17:55:20] reaction has no reactants -97: [17:55:20] reaction has no products -97: . -97: ---------------------------------------------------------------------- -97: Ran 54 tests in 0.151s -97: -97: OK -97: ******************************************** -97: /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/testData/AmideBond.rxn -97: -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 68: Test 68: -68: Sotorasib_atropBad2.mrv +68: EmbeddedSgroupSUP_MULTICENTER.mrv 68: -68: [17:55:20] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 - 98/236 Test #138: molTransformsTestCatch ................. Passed 0.04 sec -test 140 - Start 140: forceFieldHelpersCatch - -140: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/forceFieldHelpersCatch -140: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers -140: Test timeout computed to be: 1500 -125: Warning: Atom Count for residue GLU150A does not match expected count -125: Warning: Atom Count for residue ASN157A does not match expected count -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -137: *********************************************************** -137: Testing MolTransforms -137: --------------------------------- -137: test1Canonicalization -137: -137: --------------------------------- -137: testGetSetBondLength -137: -137: --------------------------------- -137: testGetSetAngle -137: -137: --------------------------------- -137: testGetSetDihedral -137: -137: --------------------------------- -137: testGetSetDihedralThroughTripleBond -137: -137: --------------------------------- -137: testGithub1262: PMI descriptors incorrect -137: -137: --------------------------------- -137: testGithub1908: CanonicalizeMol() distorting bond lengths -137: -137: --------------------------------- -137: testGithub4302: native computeCanonicalTransform() generates non-canonical coords -137: -137: --------------------------------- -137: testWeightedCentroid -137: -137: *********************************************************** -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator - 99/236 Test #137: testMolTransforms ...................... Passed 0.07 sec -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -test 141 - Start 141: testMMFFForceFieldHelpers - -141: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpers -141: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF -141: Test timeout computed to be: 1500 -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -132: Randomness seeded to: 1783321864 -132: =============================================================================== -132: All tests passed (2737 assertions in 7 test cases) -132: -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -100/236 Test #132: fpGenTestCatch ......................... Passed 0.14 sec -test 142 - Start 142: testMMFFForceFieldHelpersMultiThread - -142: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpersMultiThread -142: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF -142: Test timeout computed to be: 1500 -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: 300 -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator 68: Test 68: -68: Sotorasib_3d.mrv +68: EmbeddedSgroupSUP_SUP.mrv 68: 68: Test 68: -68: ZM374979_atrop1.mrv +68: EmbeddedSgroupSUP_SUP2.mrv 68: 68: Test 68: -68: ZM374979_atrop2.mrv +68: RgroupBad.mrv 68: 68: Test 68: -68: ZM374979_atrop3.mrv +68: valenceLessThanDrawn.mrv 68: 68: Test 68: -68: ZM374979_atropBad1.mrv +68: data_sgroup_no_fieldname.mrv 68: -68: [17:55:20] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -140: Randomness seeded to: 772586661 -140: =============================================================================== -140: All tests passed (17 assertions in 2 test cases) -140: -141: [17:55:20] ------------------------------------- -141: [17:55:20] Test MMFF atom types. -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -101/236 Test #140: forceFieldHelpersCatch ................. Passed 0.04 sec -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -test 143 - Start 143: testUFFForceFieldHelpers - -143: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF/testUFFForceFieldHelpers -143: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF -143: Test timeout computed to be: 1500 -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -102/236 Test #97: pyChemReactions ........................ Passed 0.56 sec -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -test 144 - Start 144: testCrystalForceField - -144: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalForceField -144: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF -144: Test timeout computed to be: 1500 -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -142: [17:55:20] ------------------------------------- -142: [17:55:20] Test MMFF multithreading -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -141: [17:55:20] done -141: [17:55:20] ------------------------------------- -141: [17:55:20] Testing MMFF builder tools. -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -144: ------------------------------------- -144: Test CrystalFF torsional term. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -30: ... -30: ---------------------------------------------------------------------- -30: Ran 12 tests in 0.611s -30: -30: OK -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -141: [17:55:20] done -141: [17:55:20] ------------------------------------- -141: [17:55:20] Testing MMFF builder+minimization. -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator 68: Test 68: -68: mrtx1719_3d.mrv +68: data_sgroup_empty_field_data.mrv 68: 68: Test 68: -68: mrtx1719_atrop1.mrv +68: radical_value.mrv 68: 68: Test 68: -68: mrtx1719_atrop2.mrv +68: emptyOneLineAtomList.mrv 68: 68: Test 68: -68: mrtx1719_atrop3.mrv +68: mrvValence_value.mrv 68: 68: Test 68: -68: mrtx1719_atropBad1.mrv +68: ChiralTest2.mrv 68: -68: [17:55:20] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [17:55:20] ------------------------------------- -143: [17:55:20] Test UFF atom labels. -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] done -128: [17:55:20] ------------------------------------- -128: [17:55:20] Test Hashed Atom Pairs. -128: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [17:55:20] done -128: [17:55:20] ------------------------------------- -128: [17:55:20] Test Hashed torsions. -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] done -128: [17:55:20] ------------------------------------- -128: [17:55:20] Test Rooted Atom Pairs. -128: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [17:55:20] done -128: [17:55:20] ------------------------------------- -128: [17:55:20] Test ignoring atoms in Atom Pairs. -128: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [17:55:20] done -128: [17:55:20] ------------------------------------- -128: [17:55:20] Test Rooted Topological Torsions. -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] done -128: [17:55:20] ------------------------------------- -128: [17:55:20] Test ignoring atoms in Topological Torsions. -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] done -128: [17:55:20] ------------------------------------- -128: [17:55:20] Test atom info from morgan fingerprints. -128: [17:55:20] done -128: [17:55:20] ------------------------------------- -128: [17:55:20] Test atom info from morgan fingerprints including Info Redundant Environments. -128: [17:55:20] done -128: [17:55:20] ------------------------------------- -128: [17:55:20] ------------------------------------- -128: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -112: [17:55:20] done -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -92: Randomness seeded to: 3060677539 -92: =============================================================================== -92: All tests passed (11480 assertions in 38 test cases) -92: -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] ------------------------------------- -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -112: [17:55:20] ------------------------------------- -112: [17:55:20] Test Github #3806: NaNs from AUTOCORR2D descriptor -112: [17:55:20] done -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -121: =>start test WHIM -121: [17:55:20] test on : 365 molecules done -103/236 Test #112: testAUTOCORR2D ......................... Passed 0.53 sec -104/236 Test #121: testWHIM ............................... Passed 0.46 sec +68: Test +68: +68: ChiralTest.mrv +68: +68: Test +68: +68: SnCl2.mrv +68: +68: Test +68: +68: SnH2Cl2.mrv +68: +68: Test +68: +68: marvin01.mrv +68: +68: Test +68: +68: marvin02.mrv +68: +68: Test +68: +68: marvin07.mrv +68: +68: Test +68: +68: marvin10.mrv +68: +68: Test +68: +68: marvin06.mrv +68: +68: Test +68: +68: marvin12.mrv +68: +68: Test +68: +68: EmptyMol.mrv +68: +68: Test +68: +68: Sparse.mrv +68: +68: Test +68: +68: Sparse2.mrv +68: +68: Test +68: +68: Sparse3.mrv +68: +68: Test +68: +68: MarvinNoCoords.mrv +68: +68: Test +68: +68: aspirin.mrv +68: +68: Test +68: +68: MarvinStereoGroupsZeros.mrv +68: +68: Test +68: +68: MarvinStereoGroupsAbs.mrv +68: +68: Test +68: +68: triphenylphosphine.mrv +68: +68: Test +68: +68: MarvinOldSuperGroupTest.mrv +68: +68: Test +68: +68: RadicalTests.mrv +68: +68: Test +68: +68: AnyBond.mrv +68: +68: Test +68: +68: cisBenzene.mrv +68: +68: Test +68: +68: DativeBond.mrv +68: +68: Test +68: +68: MultipleSgroup.mrv +68: +68: Test +68: +68: SgroupExpanded.mrv +68: +68: Test +68: +68: SgroupMultAttach.mrv +68: +68: Test +68: +68: MarvinMissingX2.mrv +68: +68: Test +68: +68: MarvinMissingY2.mrv +68: +68: Test +68: +68: DataSgroup.mrv +68: +68: Test +68: +68: MulticenterSgroup.mrv +68: +68: [14:17:39] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +68: [14:17:39] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +120: [14:17:39] done +120: [14:17:39] ------------------------------------- +120: [14:17:39] Basic NPR tests. +140: Randomness seeded to: 2349196984 +140: =============================================================================== +140: All tests passed (17 assertions in 2 test cases) +140: +105/236 Test #140: forceFieldHelpersCatch ................. Passed 0.16 sec +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. test 145 Start 145: pyForceFieldHelpers 145: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/Wrap/testHelpers.py" 145: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap 145: Test timeout computed to be: 1500 +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +141: [14:17:39] done +141: [14:17:39] ------------------------------------- +141: [14:17:39] Testing MMFF builder tools. +97: ........./build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py:745: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/testData/reaction1.no_metadata.png'> +97: png = open(fname, 'rb').read() +97: ResourceWarning: Enable tracemalloc to get the object allocation traceback +97: [14:17:39] Found a SCD/SED line with missing/empty SDT specification at line 34 +97: [14:17:39] Found a SCD/SED line with missing/empty SDT specification at line 36 +97: [14:17:39] Found a SCD/SED line with missing/empty SDT specification at line 38 +97: [14:17:39] Found a SCD/SED line with missing/empty SDT specification at line 40 +97: [14:17:39] Found a SCD/SED line with missing/empty SDT specification at line 42 +97: [14:17:39] Found a SCD/SED line with missing/empty SDT specification at line 87 +97: [14:17:39] Found a SCD/SED line with missing/empty SDT specification at line 89 +97: [14:17:39] Found a SCD/SED line with missing/empty SDT specification at line 91 +97: [14:17:39] Found a SCD/SED line with missing/empty SDT specification at line 93 +97: [14:17:39] Found a SCD/SED line with missing/empty SDT specification at line 95 +144: ------------------------------------- +144: Test CrystalFF torsional term. +98: .[14:17:39] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead +98: [14:17:39] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead +98: .[14:17:39] == testRemoveBadMatches +98: .[14:17:39] == testTimings +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +143: [14:17:40] ------------------------------------- +143: [14:17:40] Test UFF atom labels. +112: [14:17:40] done +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +141: [14:17:40] done +141: [14:17:40] ------------------------------------- +141: [14:17:40] Testing MMFF builder+minimization. +112: [14:17:40] ------------------------------------- +112: [14:17:40] Test Github #3806: NaNs from AUTOCORR2D descriptor +112: [14:17:40] done +106/236 Test #112: testAUTOCORR2D ......................... Passed 1.50 sec test 146 Start 146: testDistGeomHelpers 146: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/testDistGeomHelpers 146: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers 146: Test timeout computed to be: 1500 -128: [17:55:20] ------------------------------------- -128: [17:55:20] ------------------------------------- -128: [17:55:20] ------------------------------------- -128: [17:55:20] Test Atom Pairs including info about chirality. -128: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [17:55:20] done -128: [17:55:20] ------------------------------------- -128: [17:55:20] Test Topological Torsions including info about chirality. -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] done -128: [17:55:20] ------------------------------------- -128: [17:55:20] Test GitHub Issue 25: fingerprint backwards compatibility. -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [17:55:20] done -128: [17:55:20] ------------------------------------- -128: [17:55:20] Test GitHub Issue 151: PatternFingerprint problems -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [17:55:20] done -143: [17:55:20] ------------------------------------- -143: [17:55:20] Test UFF atom typer. -143: [17:55:20] done -143: [17:55:20] ------------------------------------- -143: [17:55:20] Testing UFF builder tools. -143: [17:55:20] done -143: [17:55:20] ------------------------------------- -143: [17:55:20] Testing UFF builder+minimization. -105/236 Test #92: testGenericGroups ...................... Passed 0.63 sec -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -test 147 - Start 147: distGeomHelpersCatch - -147: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/distGeomHelpersCatch -147: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers -147: Test timeout computed to be: 1500 -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [17:55:20] done -128: [17:55:20] ------------------------------------- -128: [17:55:20] Test 3D atom pairs. -128: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [17:55:20] done -128: [17:55:20] ------------------------------------- -128: [17:55:20] Test GitHub Issue 195: GenMACCSKeys() raises an exception with an empty molecule -128: [17:55:20] done -128: [17:55:20] ------------------------------------- -128: [17:55:20] Test multithreading with the pattern FP -128: reading molecules -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -142: processing -142: launch :0 -142: launch :1 -142: launch :2 -142: launch :3 -142: launch :4 -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -123: =>start test autocorr3D -123: [17:55:20] test on : 365 molecules done -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -106/236 Test #123: testAUTOCORR3D ......................... Passed 0.38 sec -141: [17:55:20] done -141: [17:55:20] ------------------------------------- -141: [17:55:20] Testing Issue239. -test 148 - Start 148: pyDistGeomHelpers - -148: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/DistGeomHelpers/Wrap/testDistGeom.py" -148: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap -148: Test timeout computed to be: 1500 -142: launch :5 -142: launch :6 -142: launch :7 -142: launch :8 -142: launch :9 -142: launch :10 -142: launch :11 -142: launch :12 -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +89: [14:17:40] Explicit valence for atom # 3 Al, 6, is greater than permitted +97: ..[14:17:40] SMARTS Parse Error: syntax error while parsing: boromicacid +97: [14:17:40] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' +97: [14:17:40] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide +97: [14:17:40] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' +97: [14:17:40] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride +97: [14:17:40] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' 68: Test 68: -68: AlexRxn.mrv +68: GenericSgroup.mrv 68: 68: Test 68: -68: BadReactionSign.mrv +68: MonomerSgroup.mrv 68: 68: Test 68: -68: bondArray_node.mrv +68: modification_sgroup.mrv +68: +68: Test +68: +68: copolymer_sgroup.mrv +68: +68: Test +68: +68: MultipleSgroupParentInMiddleOfAtomBlock.mrv +68: +68: Test +68: +68: EmbeddedSgroups.mrv 68: 68: Test 68: @@ -25203,680 +24509,860 @@ 68: 68: Test 68: -68: marvin04.mrv +68: MarvinBadMissingMolID.mrv +68: +68: [14:17:40] +68: +68: **** +68: Test Assert +68: Expression Failed: +68: Violation occurred on line 329 in file ./Code/GraphMol/MarvinParse/testMrvToMol.cpp +68: Failed Expression: GetExpectedValue(expectedMrvName) == outMolStr +68: ---------- +68: Stacktrace: +68: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +68: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +68: 2# 0x00005576F181999F in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +68: 3# 0x00005576F182469C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +68: 4# 0x00005576F1811A5D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +68: 5# 0x00007F71BD233CA8 in /lib/x86_64-linux-gnu/libc.so.6 +68: 6# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +68: 7# 0x00005576F1811BE1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +68: ---------- +68: **** 68: +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: 300 +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +143: [14:17:40] done +143: [14:17:40] ------------------------------------- +143: [14:17:40] Test UFF atom typer. +143: [14:17:40] done +143: [14:17:40] ------------------------------------- +143: [14:17:40] Testing UFF builder tools. +143: [14:17:40] done +143: [14:17:40] ------------------------------------- +143: [14:17:40] Testing UFF builder+minimization. +125: Warning: Atom Count for residue GLU5A does not match expected count +97: [14:17:40] reaction has no reactants +97: [14:17:40] reaction has no products +97: [14:17:40] initialization failed +97: [14:17:40] reaction has no reactants +97: [14:17:40] reaction has no products +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +97: .[14:17:40] SMARTS Parse Error: syntax error while parsing: boromicacid +97: [14:17:40] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' +97: [14:17:40] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide +97: [14:17:40] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' 68: Test 68: -68: marvin08.mrv +68: MarvinBadMissingAtomID.mrv 68: +68: Expected id, elementType for an atom definition in MRV file +97: [14:17:40] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride +97: [14:17:40] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' +97: [14:17:40] reaction has no reactants +97: [14:17:40] reaction has no products +97: [14:17:40] initialization failed +97: [14:17:40] reaction has no reactants +97: [14:17:40] reaction has no products +97: . +97: ---------------------------------------------------------------------- +97: Ran 54 tests in 0.649s +97: +97: OK +97: ******************************************** +97: /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/testData/AmideBond.rxn +97: +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 68: Test 68: -68: marvin09.mrv +68: MarvinBadX2.mrv 68: +68: The values x2 and y2 must be large floats in MRV file 68: Test 68: -68: marvin11.mrv +68: MarvinBadY2.mrv 68: +68: The values x2 and y2 must be large floats in MRV file +146: [14:17:40] ******************************************************** +146: [14:17:40] Testing DistGeomHelpers +146: [14:17:40] --------------------------------- +146: [14:17:40] test2 +146: +146: go +146: ------------------------------------- +146: 68: Test 68: -68: marvin05.mrv +68: MarvinBadStereoGroupsAbs.mrv 68: +68: Unrecognized group definition +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 68: Test 68: -68: EmptyRxn.mrv +68: MarvinBadElementType.mrv +68: +68: Test +68: +68: MarvinBadMissingBondID.mrv +68: +68: Test +68: +68: MarvinBadMissingBondAtomRefs +68: +68: Test +68: +68: MarvinBadMissingBondOrder.mrv +68: +68: bond must have one of: order, queryType, or convention in MRV File +68: Test +68: +68: MarvinBadMissingSruMolID.mrv +68: +68: Expected a molID in MRV file +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +68: Test +68: +68: MarvinBadMissingSruID.mrv +68: +68: Test +68: +68: MarvinBadMissingSruRole.mrv +68: +68: Test +68: +68: MarvinBadMissingSruAtomRef.mrv +68: +68: Test +68: +68: MarvinBadMissingSruTitle.mrv +68: +68: Test +68: +68: MarvinBadSruAtomRef.mrv +68: +68: AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +68: Test +68: +68: MarvinBadSruID.mrv +68: +68: Test +68: +68: MarvinBadSruRole.mrv +68: +68: Test +68: +68: MarvinBadSruAtomRef.mrv +68: +68: AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent +68: Test +68: +68: MarvinBadSruAtomRef.mrv +68: +68: AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent +68: Test +68: +68: MarvinBadSruConnect.mrv 68: -68: [17:55:20] initialization failed +68: Expected a connect string of "hh, ht, eu" for a SruSgroup definition in MRV file +142: processing +142: launch :0 +142: launch :1 +142: launch :2 +142: launch :3 +142: launch :4 +142: launch :5 +142: launch :6 +142: launch :7 +142: launch :8 +142: launch :9 +142: launch :10 +142: launch :11 +142: launch :12 142: launch :13 142: launch :14 142: launch :15 142: launch :16 142: launch :17 -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 142: launch :18 142: launch :19 142: launch :20 142: launch :21 142: launch :22 142: launch :23 -128: pass 1 +68: Test +68: +68: MarvinBadSupAttachAtom.mrv +68: +68: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file +89: [14:17:40] Explicit valence for atom # 4 Al, 6, is greater than permitted +68: Test +68: +68: MarvinBadSupAttachBond.mrv +68: +68: Bond specification for an AttachmentPoint definition must be in the bond array in MRV file +68: Test +68: +68: MarvinBadSupAttachOrder.mrv +68: +68: Order for an AttachmentPoint definition must be an integer in MRV file +68: Test +68: +68: MarvinBadSupAttachAtom.mrv +68: +68: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file +68: Test +68: +68: MarvinBadSupAttachAtom.mrv +68: +68: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file +68: Test +68: +68: MarvinBadSupAttachAtom.mrv +68: +68: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +68: Test +68: +68: MarvinBadSupMissingAttachBond.mrv +68: +68: No attachment point found for bond to the condensed atom in a superatomSgroup +141: [14:17:40] done +141: [14:17:40] ------------------------------------- +141: [14:17:40] Testing Issue239. +68: Test +68: +68: MarvinBadSupMissingAttachOrder.mrv +68: +68: Expected atom, order and bond, for an AttachmentPoint definition in MRV file +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +141: [14:17:40] done +141: [14:17:40] ------------------------------------- +141: [14:17:40] Testing calcEnergy with passed coords. +117: =>start test morse custom +117: [14:17:40] test on : 365 molecules done +128: pass 2 128: launch :0 128: launch :1 -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 128: launch :2 128: launch :3 -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -141: [17:55:20] done -141: [17:55:20] ------------------------------------- -141: [17:55:20] Testing calcEnergy with passed coords. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -146: [17:55:20] ******************************************************** -146: [17:55:20] Testing DistGeomHelpers -146: [17:55:20] --------------------------------- -146: [17:55:20] test2 -146: -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -146: go -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -147: Randomness seeded to: 3516215514 -146: ------------------------------------- -146: -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: 400 -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -141: [17:55:20] done -141: [17:55:20] ------------------------------------- -141: [17:55:20] Testing calcGrad. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +89: [14:17:40] Explicit valence for atom # 10 Si, 6, is greater than permitted +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +141: [14:17:40] done +141: [14:17:40] ------------------------------------- +141: [14:17:40] Testing calcGrad. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +107/236 Test #97: pyChemReactions ........................ Passed 2.07 sec +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +test 147 + Start 147: distGeomHelpersCatch + +147: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/distGeomHelpersCatch +147: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers +147: Test timeout computed to be: 1500 +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +141: [14:17:40] done +141: [14:17:40] ------------------------------------- +141: [14:17:40] Testing Issue242. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +108/236 Test #144: testCrystalForceField .................. Passed 0.48 sec +test 148 + Start 148: pyDistGeomHelpers + +148: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/DistGeomHelpers/Wrap/testDistGeom.py" +148: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap +148: Test timeout computed to be: 1500 +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +114: [14:17:40] ------------------------------------- +114: [14:17:40] Test empty molecule BCUT. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +109/236 Test #114: testBCUT ............................... Passed 1.86 sec +test 149 + Start 149: testMolAlign + +149: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/testMolAlign +149: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign +149: Test timeout computed to be: 1500 +147: Randomness seeded to: 3106171026 +141: [14:17:40] done +141: [14:17:40] ------------------------------------- +141: [14:17:40] Testing github 308: crash during MMFF parameterization . +141: [14:17:40] ------------------------------------- +141: [14:17:40] Testing SFIssue1653802. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +141: [14:17:40] done +141: [14:17:40] ------------------------------------- +141: [14:17:40] Testing SFIssue2378119. +141: [14:17:40] done +141: [14:17:40] ------------------------------------- +141: [14:17:40] Test MMFF force-field parameter getters. +141: [14:17:40] ------------------------------------- +141: [14:17:40] Test MMFF multithreading +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 68: Test 68: -68: RxnNoCoords.mrv +68: marvin03.mrv 68: 68: Test 68: -68: mrvValenceZero.mrv +68: Cubane.mrv 68: 68: Test 68: -68: condition_coordinates_mpoint.mrv +68: FalseAtropisomer.mrv 68: 68: Test 68: -68: marvin01.mrv +68: AtropEnhancedStereo.mrv 68: 68: Test 68: -68: aspirineSynthesisWithAttributes.mrv +68: AtropManyChirals.mrv 68: 68: Test 68: -68: marvin01.mrv +68: AtropManyChiralsEnhanced.mrv 68: 68: Test 68: -68: NewChiralTest +68: AtropManyChiralsEnhanced2.mrv 68: 68: Test 68: -68: NewChiralTest +68: AtropManyChiralsEnhanced3.mrv 68: 68: Test 68: -68: NewChiralTestNoChiral +68: AtropManyChiralsEnhanced4.mrv 68: 68: Test 68: -68: NewChiralTestNoChiral +68: BMS-986142_3d_chiral.mrv 68: 68: Test 68: -68: NewChiralTest2 +68: BMS-986142_3d.mrv 68: 68: Test 68: -68: NewChiralTest2 +68: BMS-986142_atrop1.mrv 68: 68: Test 68: -68: NewChiralTest2AllChiral +68: BMS-986142_atrop2.mrv 68: 68: Test 68: -68: NewChiralTest2AllChiral +68: BMS-986142_atrop3.mrv 68: 68: Test 68: -68: Vendor839 +68: BMS-986142_atrop4.mrv 68: 68: Test 68: -68: DoubleBondChain +68: BMS-986142_atrop5.mrv 68: +68: [14:17:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +68: [14:17:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +141: generating reference data +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: 400 +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 68: Test 68: -68: Na_Mg_Al_OH +68: BMS-986142_atrop6.mrv 68: 68: Test 68: -68: Pb +68: BMS-986142_atrop7.mrv 68: 68: Test 68: -68: O_Mg_Si +68: BMS-986142_atrop8.mrv 68: +68: [14:17:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +68: [14:17:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +139: ........ +139: ---------------------------------------------------------------------- +139: Ran 8 tests in 0.110s +139: +139: OK 68: Test 68: -68: SquiggleBond +68: BMS-986142_atropBad2.mrv 68: +68: [14:17:40] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +147: [14:17:40] [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)] +147: [14:17:40] [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)] +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +147: [14:17:40] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 32 31 30 33, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +147: [14:17:40] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 48 46 45 49, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +147: [14:17:40] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 36 37 38 39, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +147: [14:17:40] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 37 38 39 40, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +147: [14:17:40] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 38 39 40 41, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +147: [14:17:40] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 97 98 99 100, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +147: [14:17:40] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 98 99 100 101, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +147: [14:17:40] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 0 1 2 3, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +147: [14:17:40] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 1 2 4 5, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +147: [14:17:40] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 20 22 23 24, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +147: [14:17:40] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 22 23 25 26, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +147: [14:17:40] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 34 36 37 38, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +147: [14:17:40] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 66 67 68 69, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +147: [14:17:40] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 84 85 86 87, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +147: [14:17:40] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 96 97 98 99, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +147: [14:17:40] [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)] +134: .. +134: ---------------------------------------------------------------------- +134: Ran 2 tests in 0.115s +134: +134: OK +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +147: [14:17:40] [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)] +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +147: [14:17:40] [*:1][X3,X2:2]=[X3,X2:3][*:4]: 101 102 104 220, [(1 0), (-1 100), (1 0), (1 0), (1 0), (1 0)] +147: [14:17:40] [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)] +147: [14:17:40] [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)] +147: [14:17:40] [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)] +147: [14:17:40] [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)] +147: [14:17:40] [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)] +147: [14:17:40] [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)] +147: [14:17:40] [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)] +147: [14:17:40] [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)] +147: [14:17:40] [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)] +147: [14:17:40] [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)] +147: [14:17:40] [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)] +147: [14:17:40] [$([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)] +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +136: ....... +136: ---------------------------------------------------------------------- +136: Ran 7 tests in 0.357s +136: +136: OK +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 68: Test 68: -68: BigMacrocycle +68: JDQ443_3d.mrv 68: 68: Test 68: -68: Smiles1 +68: JDQ443_atrop1.mrv 68: -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [17:55:20] Explicit valence for atom # 9 N, 5, is greater than permitted -114: [17:55:20] ------------------------------------- -114: [17:55:20] Test empty molecule BCUT. -107/236 Test #68: testMrvToMol ........................... Passed 0.93 sec -108/236 Test #144: testCrystalForceField .................. Passed 0.13 sec -test 149 - Start 149: testMolAlign - -149: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/testMolAlign -149: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign -149: Test timeout computed to be: 1500 +68: Test +68: +68: JDQ443_atrop2.mrv +68: +68: Test +68: +68: JDQ443_atrop3.mrv +68: +68: Test +68: +68: JDQ443_atropBad1.mrv +68: +68: [14:17:40] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +143: [14:17:40] done +143: [14:17:40] ------------------------------------- +143: [14:17:40] Testing UFF special cases. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +147: [14:17:40] [$(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)] +147: [14:17:40] [$(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)] +147: [14:17:40] [$(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)] +147: [14:17:40] [$(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)] +147: [14:17:40] [$(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)] +147: [14:17:40] [$(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)] +147: [14:17:40] [$(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)] +147: [14:17:40] [$(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)] +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +147: [14:17:40] [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)] +147: [14:17:40] [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)] +147: [14:17:40] [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)] +147: [14:17:40] [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)] +147: [14:17:40] [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)] +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +143: [14:17:40] UFFTYPER: Unrecognized charge state for atom: 0 +143: [14:17:40] done +143: [14:17:40] ------------------------------------- +143: [14:17:40] Testing Issue239. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +147: [14:17:40] 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)] +147: [14:17:40] [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)] +147: [14:17:40] [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)] +147: [14:17:40] [!#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)] +147: [14:17:40] [!#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)] +147: [14:17:40] [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)] +147: [14:17:40] [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)] +147: [14:17:40] [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)] +147: [14:17:40] [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)] +147: [14:17:40] [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)] +147: [14:17:40] [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)] +147: [14:17:40] [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)] +147: [14:17:40] [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)] +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +142: done +147: ----------- +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +149: *********************************************************** +149: Testing MolAlign +149: --------------------------------- +149: test1MolAlign +149: +149: --------------------------------- +149: test1GetBestRMS +149: +149: --------------------------------- +149: test1MolWithQueryAlign +149: +149: --------------------------------- +149: test2AtomMap +149: +149: --------------------------------- +149: test3Weights +149: +149: --------------------------------- +149: testIssue241 +149: +149: *********************************************************** +110/236 Test #149: testMolAlign ........................... Passed 0.29 sec +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. test 150 Start 150: testO3AAlign 150: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/testO3AAlign 150: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign 150: Test timeout computed to be: 1500 -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -141: [17:55:20] done -141: [17:55:20] ------------------------------------- -141: [17:55:20] Testing Issue242. -109/236 Test #114: testBCUT ............................... Passed 0.62 sec -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -117: =>start test rdf custom -117: [17:55:20] test on : 365 molecules done +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +147: [14:17:40] [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)] +147: [14:17:40] [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)] +147: [14:17:40] [$([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)] +147: [14:17:40] [$([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)] +147: [14:17:40] [$(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)] +147: [14:17:40] [$(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)] +147: [14:17:40] [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)] +147: [14:17:40] [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)] +147: [14:17:40] 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)] +147: [14:17:40] 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)] +147: [14:17:40] [!#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)] +147: [14:17:40] [!#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)] +147: [14:17:40] [!#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)] +147: [14:17:40] [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)] +147: [14:17:40] [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)] +147: ----------- +142: [14:17:40] done +111/236 Test #139: pyMolTransforms ........................ Passed 0.95 sec +147: [14:17:40] [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)] +147: [14:17:40] [$([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)] test 151 Start 151: molAlignCatchTest 151: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/molAlignCatchTest 151: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign 151: Test timeout computed to be: 1500 -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -110/236 Test #30: pyForceFieldConstraints ................ Passed 3.42 sec -120: [17:55:20] done -120: [17:55:20] ------------------------------------- -120: [17:55:20] PMI edge cases. +147: [14:17:40] [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)] +147: [14:17:40] 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)] +147: ----------- +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: Elapsed time: 2.07872 s +115: Errors:0 +115: [14:17:40] test on : 500 molecules done +143: [14:17:40] done +143: [14:17:40] ------------------------------------- +143: [14:17:40] Testing calcEnergy with passed coords. +89: [14:17:40] Explicit valence for atom # 2 O, 4, is greater than permitted +68: Test +68: +68: RP-6306_atrop1.mrv +68: +68: Test +68: +68: RP-6306_atrop2.mrv +68: +68: Test +68: +68: RP-6306_atrop3.mrv +68: +68: Test +68: +68: RP-6306_atrop4.mrv +68: +68: Test +68: +68: RP-6306_atrop5.mrv +68: +68: [14:17:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +68: [14:17:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +112/236 Test #115: testEEM ................................ Passed 2.18 sec test 152 Start 152: pyMolAlign 152: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolAlign/Wrap/testMolAlign.py" 152: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/Wrap 152: Test timeout computed to be: 1500 -120: [17:55:20] done -120: [17:55:20] ------------------------------------- -120: [17:55:20] NPR edge cases. -120: [17:55:20] done -120: [17:55:20] ------------------------------------- -120: [17:55:20] 3D descriptors. -120: [17:55:20] done -120: [17:55:20] ------------------------------------- -120: [17:55:20] 3D descriptor edge cases. -120: [17:55:20] done -120: [17:55:20] ------------------------------------- -120: [17:55:20] Inertial shape factor. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -147: [17:55:20] [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)] -120: [17:55:20] done -147: [17:55:20] [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)] -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -111/236 Test #120: test3D ................................. Passed 0.59 sec +68: Test +68: +68: RP-6306_atropBad1.mrv +68: +68: [14:17:40] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +126: [14:17:40] DEPRECATION WARNING: please use AtomPairGenerator +126: [14:17:40] DEPRECATION WARNING: please use AtomPairGenerator +126: [14:17:40] DEPRECATION WARNING: please use AtomPairGenerator +126: [14:17:40] DEPRECATION WARNING: please use AtomPairGenerator +126: [14:17:40] DEPRECATION WARNING: please use AtomPairGenerator +126: [14:17:40] DEPRECATION WARNING: please use AtomPairGenerator +126: [14:17:40] DEPRECATION WARNING: please use AtomPairGenerator +126: [14:17:40] DEPRECATION WARNING: please use AtomPairGenerator +126: [14:17:40] DEPRECATION WARNING: please use AtomPairGenerator +126: [14:17:40] DEPRECATION WARNING: please use AtomPairGenerator +126: [14:17:40] DEPRECATION WARNING: please use AtomPairGenerator +126: [14:17:40] DEPRECATION WARNING: please use AtomPairGenerator +126: [14:17:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [14:17:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [14:17:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [14:17:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [14:17:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [14:17:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [14:17:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [14:17:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [14:17:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [14:17:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [14:17:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [14:17:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: ..[14:17:40] DEPRECATION WARNING: please use AtomPairGenerator +126: [14:17:40] DEPRECATION WARNING: please use AtomPairGenerator +126: [14:17:40] DEPRECATION WARNING: please use AtomPairGenerator +126: [14:17:40] DEPRECATION WARNING: please use AtomPairGenerator +126: [14:17:40] DEPRECATION WARNING: please use AtomPairGenerator +126: [14:17:40] DEPRECATION WARNING: please use AtomPairGenerator +126: .[14:17:40] DEPRECATION WARNING: please use AtomPairGenerator +126: [14:17:40] DEPRECATION WARNING: please use AtomPairGenerator +126: [14:17:40] DEPRECATION WARNING: please use AtomPairGenerator +147: ----------- +113/236 Test #136: pyPartialCharges ....................... Passed 1.09 sec +114/236 Test #142: testMMFFForceFieldHelpersMultiThread ... Passed 0.92 sec test 153 Start 153: testFeatures 153: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures 153: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures 153: Test timeout computed to be: 1500 -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -147: [17:55:20] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 32 31 30 33, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -147: [17:55:20] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 48 46 45 49, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -147: [17:55:20] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 36 37 38 39, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -147: [17:55:20] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 37 38 39 40, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -147: [17:55:20] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 38 39 40 41, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -147: [17:55:20] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 97 98 99 100, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -147: [17:55:20] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 98 99 100 101, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -147: [17:55:20] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 0 1 2 3, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -147: [17:55:20] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 1 2 4 5, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -147: [17:55:20] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 20 22 23 24, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -147: [17:55:20] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 22 23 25 26, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -147: [17:55:20] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 34 36 37 38, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -147: [17:55:20] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 66 67 68 69, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -147: [17:55:20] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 84 85 86 87, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -147: [17:55:20] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 96 97 98 99, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -147: [17:55:20] [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)] -147: [17:55:20] [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)] -147: [17:55:20] [*:1][X3,X2:2]=[X3,X2:3][*:4]: 101 102 104 220, [(1 0), (-1 100), (1 0), (1 0), (1 0), (1 0)] -147: [17:55:20] [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)] -147: [17:55:20] [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)] -147: [17:55:20] [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)] -147: [17:55:20] [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)] -147: [17:55:20] [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)] -147: [17:55:20] [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)] -147: [17:55:20] [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)] -147: [17:55:20] [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)] -147: [17:55:20] [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)] -147: [17:55:20] [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)] -147: [17:55:20] [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)] -147: [17:55:20] [$([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)] -147: [17:55:20] [$(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)] -147: [17:55:20] [$(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)] -147: [17:55:20] [$(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)] -147: [17:55:20] [$(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)] -147: [17:55:20] [$(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)] -147: [17:55:20] [$(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)] -147: [17:55:20] [$(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)] -147: [17:55:20] [$(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)] -141: [17:55:20] done -141: [17:55:20] ------------------------------------- -141: [17:55:20] Testing github 308: crash during MMFF parameterization . -141: [17:55:20] ------------------------------------- -141: [17:55:20] Testing SFIssue1653802. -141: [17:55:20] done -141: [17:55:20] ------------------------------------- -141: [17:55:20] Testing SFIssue2378119. -125: Warning: Atom Count for residue GLU5A does not match expected count -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -147: [17:55:20] [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)] -147: [17:55:20] [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)] -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -147: [17:55:20] [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)] -147: [17:55:20] [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)] -147: [17:55:20] [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)] -147: [17:55:20] 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)] -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -147: [17:55:20] [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)] -147: [17:55:20] [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)] -147: [17:55:20] [!#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)] -147: [17:55:20] [!#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)] -141: [17:55:20] done -141: [17:55:20] ------------------------------------- -141: [17:55:20] Test MMFF force-field parameter getters. -147: [17:55:20] [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)] -143: [17:55:20] done -143: [17:55:20] ------------------------------------- -143: [17:55:20] Testing UFF special cases. -147: [17:55:20] [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)] -147: [17:55:20] [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)] -147: [17:55:20] [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)] -147: [17:55:20] [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)] -147: [17:55:20] [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)] -147: [17:55:20] [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)] -141: [17:55:20] ------------------------------------- -141: [17:55:20] Test MMFF multithreading -143: [17:55:20] UFFTYPER: Unrecognized charge state for atom: 0 -147: [17:55:20] [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)] -143: [17:55:20] done -143: [17:55:20] ------------------------------------- -143: [17:55:20] Testing Issue239. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -153: [17:55:20] ------------------------------------- -153: [17:55:20] AtomType parser testing. -147: ----------- -153: [17:55:20] SMARTS Parse Error: syntax error while parsing: [$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103] -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -153: [17:55:20] SMARTS Parse Error: Failed parsing SMARTS '[$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103]' for input: '[$([!$([NH0]);N,O,$([S]),$([N,O)])]' -153: [17:55:20] done -153: [17:55:20] ------------------------------------- -153: [17:55:20] FeatureDefinition parser testing. -153: [17:55:20] done -153: [17:55:20] ------------------------------------- -153: [17:55:20] Test pulling feat defs from a string. -153: [17:55:20] done -153: [17:55:20] ------------------------------------- -153: [17:55:20] FeatureDef functionality testing. -147: [17:55:20] [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)] -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -147: [17:55:20] [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)] -147: [17:55:20] [$([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)] -147: [17:55:20] [$([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)] -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -147: [17:55:20] [$(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)] -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -147: [17:55:20] [$(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)] -147: [17:55:20] [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)] -147: [17:55:20] [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)] -147: [17:55:20] 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)] -147: [17:55:20] 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)] -147: [17:55:20] [!#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)] -147: [17:55:20] [!#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)] -147: [17:55:20] [!#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)] -147: [17:55:20] [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)] -147: [17:55:20] [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)] -147: ----------- -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [17:55:20] done -143: [17:55:20] ------------------------------------- -143: [17:55:20] Testing calcEnergy with passed coords. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -147: [17:55:20] [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)] -147: [17:55:20] [$([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)] -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: [17:55:20] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -147: [17:55:20] [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)] -69: [17:55:20] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -69: [17:55:20] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -69: [17:55:20] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -147: [17:55:20] 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)] -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: [17:55:20] deprecated group abbreviation ignored on line 24 -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -153: [17:55:20] done -153: [17:55:20] ------------------------------------- -153: [17:55:20] FeatureFactory testing. -153: [17:55:20] 1 -153: [17:55:20] 2 -153: [17:55:20] 3 -153: [17:55:20] 4 -153: [17:55:20] 5 -153: [17:55:20] 6 -153: [17:55:20] done -153: [17:55:20] ------------------------------------- -153: [17:55:20] Feature Location testing. -153: [17:55:20] done -153: [17:55:20] ------------------------------------- -153: [17:55:20] Test building a FeatureFactory from a file -153: [17:55:20] done -153: [17:55:20] ------------------------------------- -153: [17:55:20] Testing Issue 224. -153: [17:55:20] done -153: [17:55:20] ------------------------------------- -153: [17:55:20] Testing Issue 225. -153: [17:55:20] done -153: [17:55:20] ------------------------------------- -153: [17:55:20] Test Issue346 -153: [17:55:20] done -153: [17:55:20] ------------------------------------- -153: [17:55:20] Test Issue347 -153: [17:55:20] done -153: [17:55:20] ------------------------------------- -153: [17:55:20] Testing Issue 348. -153: [17:55:20] SMARTS Parse Error: syntax error while parsing: [C[C] -153: [17:55:20] SMARTS Parse Error: Failed parsing SMARTS '[C[C]' for input: '[C[C]' -153: [17:55:20] ------------------------------------- -153: [17:55:20] Testing Nested AtomType definitions. -153: [$([$([$([C;!$(C=[O,N,P,S]);!$(C#N)]),c]);R])] -153: [17:55:20] ------------------------------------- -153: [17:55:20] Testing Github Issue #252: crash when calling getPos() with no conformer. -153: [17:55:20] expect a precondition failure message below -153: [17:55:20] -153: -153: **** -153: Pre-condition Violation -153: molecule has no conformers -153: Violation occurred on line 37 in file ./Code/GraphMol/MolChemicalFeatures/MolChemicalFeature.cpp -153: Failed Expression: dp_mol->getNumConformers() -153: ---------- -153: Stacktrace: -153: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -153: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -153: 2# RDKit::MolChemicalFeature::getPos(int) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitMolChemicalFeatures.so.1 -153: 3# RDKit::MolChemicalFeature::getPos() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitMolChemicalFeatures.so.1 -153: 4# 0x0000563B65685E50 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures -153: 5# 0x0000563B6567A743 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures -153: 6# 0x00007F322A633CA8 in /lib/x86_64-linux-gnu/libc.so.6 -153: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -153: 8# 0x0000563B6567A841 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures -153: ---------- -153: **** -153: -153: [17:55:20] Done -153: [17:55:20] ------------------------------------- -153: [17:55:20] Testing github 2077: add confId argument to MolChemicalFeatureFactor::getFeaturesForMol() -153: [17:55:20] done -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -147: ----------- -69: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] -69: [17:55:20] -69: -69: **** -69: Post-condition Violation -69: Element 'Mv' not found -69: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h -69: Failed Expression: anum > -1 -69: ---------- -69: Stacktrace: -69: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -69: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -69: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 3# 0x00007FCE1F4C8531 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 4# 0x00007FCE1F4D1DFA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 5# 0x00007FCE1F4D217D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 6# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 8# RDKit::v2::FileParsers::MolFromMolFile(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 9# 0x000055BED1229C15 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 10# 0x000055BED1290372 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 11# 0x000055BED1210923 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 12# 0x00007FCE1EA33CA8 in /lib/x86_64-linux-gnu/libc.so.6 -69: 13# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -69: 14# 0x000055BED1210AD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: ---------- -69: **** -69: -141: generating reference data -143: [17:55:20] done -143: [17:55:20] ------------------------------------- -143: [17:55:20] Testing calcGrad. -112/236 Test #153: testFeatures ........................... Passed 0.04 sec test 154 Start 154: pyChemicalFeatures 154: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolChemicalFeatures/Wrap/testChemicalFeatures.py" 154: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap 154: Test timeout computed to be: 1500 -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [17:55:20] done -143: [17:55:20] ------------------------------------- -143: [17:55:20] Testing SFIssue1653802. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [17:55:20] done -143: [17:55:20] ------------------------------------- -143: [17:55:20] Testing SFIssue2378119. -143: [17:55:20] done -143: [17:55:20] ------------------------------------- -143: [17:55:20] Test UFF force-field parameter getters. -143: [17:55:20] ------------------------------------- -143: [17:55:20] Testing handling missing parameters. -143: [17:55:20] UFFTYPER: Unrecognized hybridization for atom: 0 -143: [17:55:20] UFFTYPER: Unrecognized atom type: Cu+1 (0) -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -147: ----------- -147: [17:55:20] [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)] -147: [17:55:20] [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)] -147: [17:55:20] [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)] -147: [17:55:20] [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)] -147: [17:55:20] [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)] -147: [17:55:20] [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)] -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [17:55:20] UFFTYPER: Unrecognized hybridization for atom: 0 -143: [17:55:20] UFFTYPER: Unrecognized atom type: Cu+1 (0) -147: [17:55:20] [$(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)] -147: [17:55:20] [$(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)] -147: [17:55:20] [$(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)] -147: [17:55:20] [$(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)] -147: [17:55:20] [$(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)] -147: [17:55:20] [$(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)] -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -147: [17:55:20] [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)] -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -147: [17:55:20] [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)] -147: [17:55:20] [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)] -147: [17:55:20] [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)] -147: [17:55:20] [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)] -147: [17:55:20] [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)] -143: [17:55:20] done -143: [17:55:20] ------------------------------------- -143: [17:55:20] Testing SFIssue3009337. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [17:55:20] done -143: [17:55:20] ------------------------------------- -143: [17:55:20] Test UFF multithreading -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -118: =>start test rdf -118: [17:55:20] test on : 365 molecules done -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -126: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -113/236 Test #118: testRDF ................................ Passed 0.70 sec -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -test 155 - Start 155: testShapeHelpers - -155: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/testShapeHelpers -155: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers -155: Test timeout computed to be: 1500 -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -126: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -126: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -126: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -126: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -126: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -126: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -126: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -126: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -126: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -126: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -126: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -126: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -134: .. -134: ---------------------------------------------------------------------- -134: Ran 2 tests in 0.048s -134: -134: OK -126: ..[17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -126: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -126: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -126: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -126: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -126: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -126: .[17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -126: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -126: [17:55:20] DEPRECATION WARNING: please use AtomPairGenerator -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: generating reference data -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -149: *********************************************************** -149: Testing MolAlign -149: --------------------------------- -149: test1MolAlign -149: -149: --------------------------------- -149: test1GetBestRMS -149: -149: --------------------------------- -149: test1MolWithQueryAlign -149: -149: --------------------------------- -149: test2AtomMap -149: -149: --------------------------------- -149: test3Weights -149: -149: --------------------------------- -149: testIssue241 -149: -149: *********************************************************** -126: ..[17:55:20] +130: [14:17:40] done +130: [14:17:40] ------------------------------------- +130: [14:17:40] Test unfolded version of RDKFP +130: [14:17:40] ------------------------------------- +130: [14:17:40] Test topological torsion fp generator +130: [14:17:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [14:17:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [14:17:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [14:17:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [14:17:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [14:17:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [14:17:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [14:17:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator +68: Test +68: +68: RP-6306_atropBad2.mrv +68: +68: [14:17:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +68: [14:17:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +68: [14:17:40] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +147: [14:17:40] [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)] +147: [14:17:40] [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)] +147: [14:17:40] [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)] +147: [14:17:40] [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)] +147: [14:17:40] [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)] +147: [14:17:40] [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)] +147: [14:17:40] [$(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)] +147: [14:17:40] [$(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)] +147: [14:17:40] [$(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)] +147: [14:17:40] [$(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)] +147: [14:17:40] [$(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)] +147: [14:17:40] [$(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)] +147: [14:17:40] [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)] +147: [14:17:40] [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)] +147: [14:17:40] [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)] +147: [14:17:40] [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)] +147: [14:17:40] [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)] +147: [14:17:40] [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)] +126: ..[14:17:40] 126: 126: **** -114/236 Test #149: testMolAlign ........................... Passed 0.13 sec -test 156 - Start 156: pyShapeHelpers - -156: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ShapeHelpers/Wrap/testShapeHelpers.py" -156: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap -156: Test timeout computed to be: 1500 -136: ....... -136: ---------------------------------------------------------------------- -136: Ran 7 tests in 0.106s -136: -136: OK -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: Elapsed time: 0.710573 s -115: Errors:0 -115: [17:55:20] test on : 500 molecules done 126: Pre-condition Violation 126: Number of atom props not equal to number of atoms 126: Violation occurred on line 89 in file ./Code/GraphMol/Descriptors/BCUT.cpp @@ -25886,10 +25372,10 @@ 126: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 126: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 126: 2# RDKit::Descriptors::BCUT2D(RDKit::ROMol const&, std::vector > const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitDescriptors.so.1 -126: 3# 0x00007F8BC819D43A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdMolDescriptors.so -126: 4# 0x00007F8BC81AD726 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdMolDescriptors.so +126: 3# 0x00007FE9CF4EC43A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdMolDescriptors.so +126: 4# 0x00007FE9CF4FC726 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdMolDescriptors.so 126: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -126: 6# 0x00007F8BCC1A962C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +126: 6# 0x00007FE9D34F662C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 126: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 126: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 126: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so @@ -25900,17 +25386,17 @@ 126: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 126: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 126: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -126: 17# 0x00007F8BC9DB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -126: 18# 0x00007F8BC9DB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -126: 19# 0x00007F8BC9DB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -126: 20# 0x00007F8BC9DB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -126: 21# 0x00007F8BC9DB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +126: 17# 0x00007FE9D0FB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +126: 18# 0x00007FE9D0FB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +126: 19# 0x00007FE9D0FB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +126: 20# 0x00007FE9D0FB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +126: 21# 0x00007FE9D0FB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 126: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 126: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 126: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 126: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 126: 26# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -126: 27# 0x00007F8BCC1A63C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +126: 27# 0x00007FE9D34F33C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 126: 28# _PyObject_MakeTpCall in /usr/bin/python3 126: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 126: 30# 0x00000000005CD3C9 in /usr/bin/python3 @@ -25942,55 +25428,219 @@ 126: 56# 0x00000000006B921E in /usr/bin/python3 126: 57# Py_RunMain in /usr/bin/python3 126: 58# Py_BytesMain in /usr/bin/python3 -126: 59# 0x00007F8BCCA74CA8 in /lib/x86_64-linux-gnu/libc.so.6 +126: 59# 0x00007FE9D3DC1CA8 in /lib/x86_64-linux-gnu/libc.so.6 126: 60# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 126: 61# _start in /usr/bin/python3 126: ---------- 126: **** 126: -115/236 Test #115: testEEM ................................ Passed 0.74 sec -test 157 - Start 157: testMolCatalog +89: [14:17:40] Explicit valence for atom # 3 Al, 6, is greater than permitted +89: [14:17:40] Explicit valence for atom # 3 Be, 4, is greater than permitted +133: .............. +133: ---------------------------------------------------------------------- +133: Ran 14 tests in 0.378s +133: +133: OK +143: [14:17:40] done +143: [14:17:40] ------------------------------------- +143: [14:17:40] Testing calcGrad. +153: [14:17:40] ------------------------------------- +153: [14:17:40] AtomType parser testing. +153: [14:17:40] SMARTS Parse Error: syntax error while parsing: [$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103] +153: [14:17:40] SMARTS Parse Error: Failed parsing SMARTS '[$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103]' for input: '[$([!$([NH0]);N,O,$([S]),$([N,O)])]' +153: [14:17:40] done +153: [14:17:40] ------------------------------------- +153: [14:17:40] FeatureDefinition parser testing. +153: [14:17:40] done +153: [14:17:40] ------------------------------------- +153: [14:17:40] Test pulling feat defs from a string. +153: [14:17:40] done +153: [14:17:40] ------------------------------------- +153: [14:17:40] FeatureDef functionality testing. +115/236 Test #134: pyTestMHFP ............................. Passed 1.21 sec +130: [14:17:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator +153: [14:17:40] done +153: [14:17:40] ------------------------------------- +153: [14:17:40] FeatureFactory testing. +153: [14:17:40] 1 +153: [14:17:40] 2 +153: [14:17:40] 3 +153: [14:17:40] 4 +153: [14:17:40] 5 +153: [14:17:40] 6 +153: [14:17:40] done +153: [14:17:40] ------------------------------------- +153: [14:17:40] Feature Location testing. +153: [14:17:40] done +153: [14:17:40] ------------------------------------- +153: [14:17:40] Test building a FeatureFactory from a file +153: [14:17:40] done +153: [14:17:40] ------------------------------------- +153: [14:17:40] Testing Issue 224. +153: [14:17:40] done +153: [14:17:40] ------------------------------------- +153: [14:17:40] Testing Issue 225. +153: [14:17:40] done +153: [14:17:40] ------------------------------------- +153: [14:17:40] Test Issue346 +145: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [14:17:40] Molecule does not have explicit Hs. Consider calling AddHs() +145: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [14:17:40] Molecule does not have explicit Hs. Consider calling AddHs() +145: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [14:17:40] Molecule does not have explicit Hs. Consider calling AddHs() +145: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [14:17:40] Molecule does not have explicit Hs. Consider calling AddHs() +145: [14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [14:17:40] Molecule does not have explicit Hs. Consider calling AddHs() +145: ..[14:17:40] Molecule does not have explicit Hs. Consider calling AddHs() +test 155 + Start 155: testShapeHelpers -157: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/testMolCatalog -157: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog -157: Test timeout computed to be: 1500 -139: ........ -139: ---------------------------------------------------------------------- -139: Ran 8 tests in 0.034s -139: -139: OK -151: Randomness seeded to: 3730275458 -151: 56986440 +155: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/testShapeHelpers +155: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers +155: Test timeout computed to be: 1500 +130: [14:17:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [14:17:40] done +130: [14:17:40] ------------------------------------- +130: [14:17:40] Test Topological Torsions. +130: [14:17:40] done +130: [14:17:40] ------------------------------------- +130: [14:17:40] Test Folded torsions. +130: [14:17:40] done +130: [14:17:40] ------------------------------------- +130: [14:17:40] Test Bulk Topological Torsions. +153: [14:17:40] done +153: [14:17:40] ------------------------------------- +153: [14:17:40] Test Issue347 +153: [14:17:40] done +153: [14:17:40] ------------------------------------- +153: [14:17:40] Testing Issue 348. +153: [14:17:40] SMARTS Parse Error: syntax error while parsing: [C[C] +153: [14:17:40] SMARTS Parse Error: Failed parsing SMARTS '[C[C]' for input: '[C[C]' +153: [14:17:40] ------------------------------------- +153: [14:17:40] Testing Nested AtomType definitions. +153: [$([$([$([C;!$(C=[O,N,P,S]);!$(C#N)]),c]);R])] +153: [14:17:40] ------------------------------------- +153: [14:17:40] Testing Github Issue #252: crash when calling getPos() with no conformer. +153: [14:17:40] expect a precondition failure message below +153: [14:17:40] +153: +153: **** +153: Pre-condition Violation +153: molecule has no conformers +153: Violation occurred on line 37 in file ./Code/GraphMol/MolChemicalFeatures/MolChemicalFeature.cpp +153: Failed Expression: dp_mol->getNumConformers() +153: ---------- +153: Stacktrace: +153: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +153: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +153: 2# RDKit::MolChemicalFeature::getPos(int) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitMolChemicalFeatures.so.1 +153: 3# RDKit::MolChemicalFeature::getPos() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitMolChemicalFeatures.so.1 +153: 4# 0x0000557C52665E50 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures +153: 5# 0x0000557C5265A743 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures +153: 6# 0x00007F88E9033CA8 in /lib/x86_64-linux-gnu/libc.so.6 +153: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +153: 8# 0x0000557C5265A841 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures +153: ---------- +153: **** +153: +153: [14:17:40] Done +153: [14:17:40] ------------------------------------- +153: [14:17:40] Testing github 2077: add confId argument to MolChemicalFeatureFactor::getFeaturesForMol() +153: [14:17:40] done +145: [14:17:40] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [14:17:40] Molecule does not have explicit Hs. Consider calling AddHs() +116/236 Test #153: testFeatures ........................... Passed 0.08 sec +test 156 + Start 156: pyShapeHelpers + +156: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ShapeHelpers/Wrap/testShapeHelpers.py" +156: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap +156: Test timeout computed to be: 1500 +143: [14:17:40] done +143: [14:17:40] ------------------------------------- +143: [14:17:40] Testing SFIssue1653802. +143: [14:17:40] done +143: [14:17:40] ------------------------------------- +143: [14:17:40] Testing SFIssue2378119. +143: [14:17:40] done +143: [14:17:40] ------------------------------------- +143: [14:17:40] Test UFF force-field parameter getters. +143: [14:17:40] ------------------------------------- +145: .[14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [14:17:40] Molecule does not have explicit Hs. Consider calling AddHs() +143: [14:17:40] Testing handling missing parameters. +143: [14:17:40] UFFTYPER: Unrecognized hybridization for atom: 0 +143: [14:17:40] UFFTYPER: Unrecognized atom type: Cu+1 (0) +143: [14:17:40] UFFTYPER: Unrecognized hybridization for atom: 0 +143: [14:17:40] UFFTYPER: Unrecognized atom type: Cu+1 (0) 126: ...Warning: Atom Count for residue GLU5A does not match expected count +68: Test +68: +68: RP-6306_3d.mrv +68: +68: Test +68: +68: Sotorasib_atrop1.mrv +68: +68: Test +68: +68: Sotorasib_atrop2.mrv +68: +68: Test +68: +68: Sotorasib_atrop3.mrv +68: +68: Test +68: +68: Sotorasib_atrop4.mrv +68: +68: Test +68: +68: Sotorasib_atrop5.mrv +68: +68: [14:17:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +68: [14:17:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 126: Warning: Atom Count for residue ASN39A does not match expected count +143: [14:17:40] done +143: [14:17:40] ------------------------------------- +143: [14:17:40] Testing SFIssue3009337. +148: .[14:17:40] Molecule does not have explicit Hs. Consider calling AddHs() +89: [14:17:40] Explicit valence for atom # 27 P, 6, is greater than permitted +68: Test +68: +68: Sotorasib_atropBad1.mrv +68: +68: [14:17:40] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 126: Warning: Atom Count for residue GLU53A does not match expected count 126: Warning: Atom Count for residue ARG64A does not match expected count 126: Warning: Atom Count for residue LYS80A does not match expected count -126: Warning: Atom Count for residue GLU150A does not match expected count -126: Warning: Atom Count for residue ASN157A does not match expected count -116/236 Test #136: pyPartialCharges ....................... Passed 0.41 sec -test 158 - Start 158: pyMolCatalog - -158: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolCatalog/Wrap/rough_test.py" -158: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/Wrap -158: Test timeout computed to be: 1500 -89: [17:55:20] Explicit valence for atom # 3 Al, 6, is greater than permitted -130: [17:55:20] done -130: [17:55:20] ------------------------------------- -130: [17:55:20] Test unfolded version of RDKFP -130: [17:55:20] ------------------------------------- -130: [17:55:20] Test topological torsion fp generator -130: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -142: done -130: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -117/236 Test #134: pyTestMHFP ............................. Passed 0.44 sec +109: [14:17:40] +109: +109: **** +109: Invariant Violation +109: nonsense +109: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp +109: Failed Expression: token != tokens.end() +109: ---------- +109: Stacktrace: +109: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +109: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +109: 2# 0x00007F7C07715DFD in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 +109: 3# RDKit::readFuncGroups(std::istream&, int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 +109: 4# 0x000055564C8D01FC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 5# 0x000055564C8CD6A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 6# 0x00007F7C06A33CA8 in /lib/x86_64-linux-gnu/libc.so.6 +109: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +109: 8# 0x000055564C8CD7D1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: ---------- +109: **** +109: +143: [14:17:40] done +143: [14:17:40] ------------------------------------- +143: [14:17:40] Test UFF multithreading 155: *********************************************************** 155: Testing ShapeHelpers 155: --------------------------------- @@ -26003,188 +25653,445 @@ 155: testGithub4364 155: 155: *********************************************************** -test 159 - Start 159: moldraw2DTest1 - -159: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTest1 -159: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D -159: Test timeout computed to be: 1500 -151: 37451824 -118/236 Test #155: testShapeHelpers ....................... Passed 0.07 sec -119/236 Test #157: testMolCatalog ......................... Passed 0.04 sec -test 160 - Start 160: moldraw2DTestCatch - -160: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D -160: Test timeout computed to be: 1500 -test 161 - Start 161: moldraw2DRxnTest1 - -161: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DRxnTest1 -161: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D -161: Test timeout computed to be: 1500 -130: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -142: [17:55:20] done -120/236 Test #139: pyMolTransforms ........................ Passed 0.40 sec -test 162 - Start 162: pyMolDraw2D +117/236 Test #133: pyTestGenerator ........................ Passed 1.38 sec +test 157 + Start 157: testMolCatalog -162: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/Wrap/testMolDraw2D.py" -162: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap -162: Test timeout computed to be: 1500 -128: pass 2 -128: launch :0 -128: launch :1 -128: launch :2 -128: launch :3 -130: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [17:55:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [17:55:20] done -130: [17:55:20] ------------------------------------- -130: [17:55:20] Test Topological Torsions. -130: [17:55:20] done -130: [17:55:20] ------------------------------------- -130: [17:55:20] Test Folded torsions. -130: [17:55:20] done -130: [17:55:20] ------------------------------------- -130: [17:55:20] Test Bulk Topological Torsions. -121/236 Test #142: testMMFFForceFieldHelpersMultiThread ... Passed 0.38 sec -109: [17:55:20] +157: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/testMolCatalog +157: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog +157: Test timeout computed to be: 1500 +151: Randomness seeded to: 3462247664 +151: 60145481 +109: [14:17:40] 109: 109: **** 109: Invariant Violation -109: nonsense +109: nonsense no new line 109: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp 109: Failed Expression: token != tokens.end() 109: ---------- 109: Stacktrace: 109: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 109: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -109: 2# 0x00007FA6F2902DFD in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 +109: 2# 0x00007F7C07715DFD in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 109: 3# RDKit::readFuncGroups(std::istream&, int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 -109: 4# 0x000055D2E9C6F1FC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 5# 0x000055D2E9C6C6A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 6# 0x00007FA6F1C33CA8 in /lib/x86_64-linux-gnu/libc.so.6 +109: 4# 0x000055564C8D01FC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 5# 0x000055564C8CD6A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 6# 0x00007F7C06A33CA8 in /lib/x86_64-linux-gnu/libc.so.6 109: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -109: 8# 0x000055D2E9C6C7D1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 8# 0x000055564C8CD7D1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 109: ---------- 109: **** 109: -109: [17:55:20] +109: [14:17:40] 109: 109: **** 109: Invariant Violation -109: nonsense no new line +109: nonsense with tab 109: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp 109: Failed Expression: token != tokens.end() 109: ---------- 109: Stacktrace: 109: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 109: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -109: 2# 0x00007FA6F2902DFD in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 +109: 2# 0x00007F7C07715DFD in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 109: 3# RDKit::readFuncGroups(std::istream&, int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 -109: 4# 0x000055D2E9C6F1FC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 5# 0x000055D2E9C6C6A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 6# 0x00007FA6F1C33CA8 in /lib/x86_64-linux-gnu/libc.so.6 +109: 4# 0x000055564C8D01FC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 5# 0x000055564C8CD6A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 6# 0x00007F7C06A33CA8 in /lib/x86_64-linux-gnu/libc.so.6 109: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -109: 8# 0x000055D2E9C6C7D1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 8# 0x000055564C8CD7D1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 109: ---------- 109: **** 109: -109: [17:55:20] -109: -109: **** +118/236 Test #109: testFragCatalog ........................ Passed 2.48 sec +119/236 Test #155: testShapeHelpers ....................... Passed 0.11 sec +test 158 + Start 158: pyMolCatalog + +158: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolCatalog/Wrap/rough_test.py" +158: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/Wrap +158: Test timeout computed to be: 1500 +test 159 + Start 159: moldraw2DTest1 + +159: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTest1 +159: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D +159: Test timeout computed to be: 1500 +68: Test +68: +68: Sotorasib_atropBad2.mrv +68: +68: [14:17:40] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +148: [14:17:40] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:17:40] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:17:40] Molecule does not have explicit Hs. Consider calling AddHs() +148: ..[14:17:40] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:17:40] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:17:40] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:17:40] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:17:40] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:17:40] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:17:40] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:17:40] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:17:40] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:17:40] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:17:40] Molecule does not have explicit Hs. Consider calling AddHs() +148: ..[14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +148: .[14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +126: Warning: Atom Count for residue GLU150A does not match expected count +126: Warning: Atom Count for residue ASN157A does not match expected count +145: .[14:17:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [14:17:40] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[14:17:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +118: =>start test rdf +118: [14:17:40] test on : 365 molecules done +120/236 Test #118: testRDF ................................ Passed 2.32 sec +148: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[14:17:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[14:17:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[14:17:41] UFFTYPER: Unrecognized hybridization for atom: 0 +145: [14:17:41] UFFTYPER: Unrecognized atom type: Cu+1 (0) +145: .[14:17:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +145: [14:17:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +145: [14:17:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +145: [14:17:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +143: generating reference data +test 160 + Start 160: moldraw2DTestCatch + +160: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D +160: Test timeout computed to be: 1500 +121/236 Test #157: testMolCatalog ......................... Passed 0.11 sec +148: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +145: [14:17:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[14:17:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[14:17:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +145: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +145: ...[14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +145: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +test 161 + Start 161: moldraw2DRxnTest1 + +161: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DRxnTest1 +161: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D +161: Test timeout computed to be: 1500 +151: 106721756 +148: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +120: [14:17:41] done +120: [14:17:41] ------------------------------------- +120: [14:17:41] PMI edge cases. +120: [14:17:41] done +120: [14:17:41] ------------------------------------- +120: [14:17:41] NPR edge cases. +159: ----------------- Test 1 +120: [14:17:41] done +120: [14:17:41] ------------------------------------- +120: [14:17:41] 3D descriptors. +120: [14:17:41] done +120: [14:17:41] ------------------------------------- +120: [14:17:41] 3D descriptor edge cases. +120: [14:17:41] done +120: [14:17:41] ------------------------------------- +120: [14:17:41] Inertial shape factor. +148: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +120: [14:17:41] done +122/236 Test #120: test3D ................................. Passed 2.38 sec +148: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +test 162 + Start 162: pyMolDraw2D + +162: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/Wrap/testMolDraw2D.py" +162: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap +162: Test timeout computed to be: 1500 +147: [14:17:41] UFFTYPER: Unrecognized atom type: Pt5+2 (1) +145: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +117: =>start test AUTOCORR3D custom +117: [14:17:41] test on : 365 molecules done +161: ----------------- Test 1 +159: file test1_5.svg gave hash 2383324771U not the expected 2811480876U +159: Done +159: ----------------- Test 2 +147: [14:17:41] UFFTYPER: Unrecognized charge state for atom: 1 +147: [14:17:41] UFFTYPER: Unrecognized charge state for atom: 1 +148: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +159: file test2_1.png gave hash 240594419U not the expected 638584804U +126: Warning: Atom Count for residue GLU5A does not match expected count +145: ... +145: ---------------------------------------------------------------------- +145: Ran 19 tests in 0.436s +145: +145: OK +148: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +68: Test +68: +68: Sotorasib_3d.mrv +68: +68: Test +68: +68: ZM374979_atrop1.mrv +68: +68: Test +68: +68: ZM374979_atrop2.mrv +68: +68: Test +68: +68: ZM374979_atrop3.mrv +68: +68: Test +68: +68: ZM374979_atropBad1.mrv +68: +68: [14:17:41] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +161: file rxn_test1_1.png gave hash 760679292U not the expected 801892091U +159: file test2_2.png gave hash 278647755U not the expected 610424244U +147: [14:17:41] UFFTYPER: Unrecognized charge state for atom: 1 +160: Randomness seeded to: 3757980912 +160: file testAtomTags_3.svg gave hash 1931256064U not the expected 2244078420U +159: Done +159: ----------------- Test 4 +159: file test4_1.png gave hash 509333604U not the expected 3993974247U +159: Done +159: ----------------- Test 5 +148: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +141: processing +141: launch :0 +141: launch :1 +141: launch :2 +141: [14:17:41] Rep: 0 Mol:0 +141: launch :3 +148: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +141: [14:17:41] Rep: 0 Mol:1 +161: file rxn_test1_2.png gave hash 3312211595U not the expected 507435337U +141: [14:17:41] Rep: 0 Mol:4 +141: [14:17:41] Rep: 0 Mol:5 +141: [14:17:41] Rep: 0 Mol:2 +159: file test5_1.png gave hash 650561118U not the expected 571291290U +141: [14:17:41] Rep: 0 Mol:9 +141: [14:17:41] Rep: 0 Mol:3 +141: [14:17:41] Rep: 0 Mol:13 +119: =>start test MORSE +119: =>read file +119: [14:17:41] test on : 365 molecules done +69: [14:17:41] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +69: [14:17:41] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +141: [14:17:41] Rep: 0 Mol:17 +141: [14:17:41] Rep: 0 Mol:8 +69: [14:17:41] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +69: [14:17:41] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +123/236 Test #119: testMORSE .............................. Passed 2.66 sec test 163 Start 163: testFMCS 163: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/testFMCS 163: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FMCS 163: Test timeout computed to be: 1500 -109: Invariant Violation -109: nonsense with tab -109: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp -109: Failed Expression: token != tokens.end() -109: ---------- -109: Stacktrace: -109: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -109: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -109: 2# 0x00007FA6F2902DFD in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 -109: 3# RDKit::readFuncGroups(std::istream&, int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 -109: 4# 0x000055D2E9C6F1FC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 5# 0x000055D2E9C6C6A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 6# 0x00007FA6F1C33CA8 in /lib/x86_64-linux-gnu/libc.so.6 -109: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -109: 8# 0x000055D2E9C6C7D1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: ---------- -109: **** -109: -145: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -122/236 Test #109: testFragCatalog ........................ Passed 0.85 sec +117: =>start test 2 WHIM custom +117: [14:17:41] test on : 365 molecules done +141: [14:17:41] Rep: 0 Mol:12 +141: [14:17:41] Rep: 0 Mol:21 +141: [14:17:41] Rep: 0 Mol:16 +124/236 Test #145: pyForceFieldHelpers .................... Passed 1.43 sec +130: [14:17:41] done +130: [14:17:41] ------------------------------------- +130: [14:17:41] Test Rooted Topological Torsions. +130: [14:17:41] done +130: [14:17:41] ------------------------------------- +130: [14:17:41] Test ignoring atoms in Topological Torsions. +130: [14:17:41] done +130: [14:17:41] ------------------------------------- +130: [14:17:41] ------------------------------------- +130: [14:17:41] Test Topological Torsions including info about chirality. +130: [14:17:41] done +130: [14:17:41] ------------------------------------- +130: [14:17:41] Test GitHub Issue 25: fingerprint backwards compatibility. +130: [14:17:41] done +130: [14:17:41] ------------------------------------- +130: [14:17:41] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. +130: [14:17:41] done +130: [14:17:41] ------------------------------------- +130: [14:17:41] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 +141: [14:17:41] Rep: 0 Mol:25 +141: [14:17:41] Rep: 0 Mol:20 +141: [14:17:41] Rep: 0 Mol:29 +141: [14:17:41] Rep: 0 Mol:6 +141: [14:17:41] Rep: 0 Mol:24 +141: [14:17:41] Rep: 0 Mol:28 +148: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +160: file contourMol_1.svg gave hash 4125787245U not the expected 3634867913U +159: file test5_2.png gave hash 2649140411U not the expected 97265124U test 164 Start 164: pyFMCS 164: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/Wrap/testFMCS.py" 164: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Wrap 164: Test timeout computed to be: 1500 -145: [17:55:20] Molecule does not have explicit Hs. Consider calling AddHs() -145: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [17:55:20] Molecule does not have explicit Hs. Consider calling AddHs() -145: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [17:55:20] Molecule does not have explicit Hs. Consider calling AddHs() -145: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [17:55:20] Molecule does not have explicit Hs. Consider calling AddHs() -145: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [17:55:20] Molecule does not have explicit Hs. Consider calling AddHs() -145: ..[17:55:20] Molecule does not have explicit Hs. Consider calling AddHs() -145: [17:55:20] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [17:55:20] Molecule does not have explicit Hs. Consider calling AddHs() -69: [17:55:20] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -69: [17:55:20] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -89: [17:55:20] Explicit valence for atom # 4 Al, 6, is greater than permitted -126: Warning: Atom Count for residue GLU5A does not match expected count -145: .[17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [17:55:20] Molecule does not have explicit Hs. Consider calling AddHs() -159: ----------------- Test 1 -133: .............. -133: ---------------------------------------------------------------------- -133: Ran 14 tests in 0.124s -133: -133: OK -161: ----------------- Test 1 -147: [17:55:20] UFFTYPER: Unrecognized atom type: Pt5+2 (1) -147: [17:55:20] UFFTYPER: Unrecognized charge state for atom: 1 -160: Randomness seeded to: 2055708869 -160: file testAtomTags_3.svg gave hash 1931256064U not the expected 2244078420U -89: [17:55:20] Explicit valence for atom # 10 Si, 6, is greater than permitted -145: .[17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [17:55:20] Molecule does not have explicit Hs. Consider calling AddHs() -147: [17:55:20] UFFTYPER: Unrecognized charge state for atom: 1 -119: =>start test MORSE -119: =>read file -119: [17:55:20] test on : 365 molecules done -147: [17:55:20] UFFTYPER: Unrecognized charge state for atom: 1 -123/236 Test #119: testMORSE .............................. Passed 0.86 sec -145: .[17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -159: file test1_5.svg gave hash 2383324771U not the expected 2811480876U +130: [14:17:41] done +130: [14:17:41] ------------------------------------- +130: [14:17:41] Test convenience and bulk fp calculation functions +141: [14:17:41] Rep: 0 Mol:10 +160: file contourMol_2.svg gave hash 4241964660U not the expected 1815941817U +159: file test5_3.png gave hash 2951986966U not the expected 606188176U +69: [14:17:41] deprecated group abbreviation ignored on line 24 +161: file rxn_test1_3.png gave hash 288594716U not the expected 1590809137U +69: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] +69: [14:17:41] +69: +69: **** +69: Post-condition Violation +69: Element 'Mv' not found +69: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h +69: Failed Expression: anum > -1 +69: ---------- +69: Stacktrace: +69: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +69: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +69: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 3# 0x00007FECAF2C8531 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 4# 0x00007FECAF2D1DFA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 5# 0x00007FECAF2D217D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 6# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 8# RDKit::v2::FileParsers::MolFromMolFile(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 9# 0x000055AD5A891C15 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 10# 0x000055AD5A8F8372 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 11# 0x000055AD5A878923 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 12# 0x00007FECAE833CA8 in /lib/x86_64-linux-gnu/libc.so.6 +69: 13# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +69: 14# 0x000055AD5A878AD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: ---------- +69: **** +69: +141: [14:17:41] Rep: 0 Mol:7 +141: [14:17:41] Rep: 0 Mol:11 +141: [14:17:41] Rep: 0 Mol:15 +148: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +159: Done +159: ----------------- Test 6 (atom labels) +141: [14:17:41] Rep: 0 Mol:19 +141: [14:17:41] Rep: 0 Mol:23 +141: [14:17:41] Rep: 0 Mol:27 +127: ........ +127: ---------------------------------------------------------------------- +127: Ran 8 tests in 1.174s +127: +127: OK +141: [14:17:41] Rep: 0 Mol:31 +158: . +158: ---------------------------------------------------------------------- +158: Ran 1 test in 0.011s +158: +158: OK +141: [14:17:41] Rep: 0 Mol:14 +161: file rxn_test1_4.png gave hash 1996676260U not the expected 1766700542U +68: Test +68: +68: mrtx1719_3d.mrv +68: +68: Test +68: +68: mrtx1719_atrop1.mrv +68: +68: Test +68: +68: mrtx1719_atrop2.mrv +68: +68: Test +68: +68: mrtx1719_atrop3.mrv +68: +68: Test +68: +68: mrtx1719_atropBad1.mrv +68: +68: [14:17:41] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +159: Done +159: ----------------- Test 7 (backgrounds) +160: file contourMol_3.svg gave hash 1333854566U not the expected 2579392727U +141: [14:17:41] Rep: 0 Mol:18 +141: [14:17:41] Rep: 0 Mol:22 +141: [14:17:41] Rep: 0 Mol:26 +141: [14:17:41] Rep: 0 Mol:30 +125: Warning: Atom Count for residue ASN39A does not match expected count +160: file contourMol_4.svg gave hash 4249475618U not the expected 2914799663U +161: file rxn_test1_5.png gave hash 1068409486U not the expected 2552100594U +159: file test7_1.png gave hash 2406197059U not the expected 1322246680U +125/236 Test #158: pyMolCatalog ........................... Passed 0.62 sec test 165 Start 165: FMCStest 165: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test/FMCStest 165: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test 165: Test timeout computed to be: 1500 -145: [17:55:20] Molecule does not have explicit Hs. Consider calling AddHs() +141: [14:17:41] Rep: 20 Mol:1 +141: [14:17:41] Rep: 20 Mol:5 +141: [14:17:41] Rep: 20 Mol:9 +159: file test7_2.png gave hash 4033628357U not the expected 1499012715U 159: Done -159: ----------------- Test 2 -161: file rxn_test1_1.png gave hash 760679292U not the expected 801892091U -124/236 Test #133: pyTestGenerator ........................ Passed 0.59 sec -test 166 - Start 166: molHashCatchTest - -166: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/molHashCatchTest -166: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolHash -166: Test timeout computed to be: 1500 +159: ----------------- Test8: PrepareMolDrawing +160: file contourMol_5.svg gave hash 3954963517U not the expected 3792684719U +147: [14:17:41] UFFTYPER: Unrecognized charge state for atom: 5 +159: Done +159: ----------------- Test multi-threaded drawing +159: reading molecules +141: [14:17:41] Rep: 20 Mol:13 +141: [14:17:41] Rep: 20 Mol:17 +141: [14:17:41] Rep: 20 Mol:21 +141: [14:17:41] Rep: 20 Mol:25 +148: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +141: [14:17:41] Rep: 20 Mol:29 +147: [14:17:41] UFFTYPER: Unrecognized charge state for atom: 5 +154: .[14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory @@ -27884,31 +27791,6 @@ 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_51_54554.txt 165: -145: .[17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [17:55:20] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [17:55:20] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[17:55:20] UFFTYPER: Unrecognized hybridization for atom: 0 -145: [17:55:20] UFFTYPER: Unrecognized atom type: Cu+1 (0) -145: .[17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [17:55:20] Molecule does not have explicit Hs. Consider calling AddHs() -145: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [17:55:20] Molecule does not have explicit Hs. Consider calling AddHs() -145: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [17:55:20] Molecule does not have explicit Hs. Consider calling AddHs() -145: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [17:55:20] Molecule does not have explicit Hs. Consider calling AddHs() -145: [17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [17:55:20] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [17:55:20] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[17:55:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [17:55:20] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[17:55:20] Molecule does not have explicit Hs. Consider calling AddHs() -145: [17:55:20] Molecule does not have explicit Hs. Consider calling AddHs() -145: ...[17:55:20] Molecule does not have explicit Hs. Consider calling AddHs() -145: [17:55:20] Molecule does not have explicit Hs. Consider calling AddHs() -145: [17:55:20] Molecule does not have explicit Hs. Consider calling AddHs() 165: testChEMBL_Txt() chembl_II_sets/Target_no_51_57508.txtfopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory @@ -28175,256 +28057,267 @@ 165: 165: testFileSDF_RandomSet(): benchmark/chembl13_threshold_90.smi 165: ERROR: RDKit could not load input file -159: file test2_1.png gave hash 240594419U not the expected 638584804U -159: file test2_2.png gave hash 278647755U not the expected 610424244U -159: Done -159: ----------------- Test 4 -159: file test4_1.png gave hash 509333604U not the expected 3993974247U -159: Done -159: ----------------- Test 5 -60: Test -60: -60: AtropCanon1.cxsmi -60: -60: Test -60: -60: AtropCanon2.cxsmi -60: -60: Test -60: -60: AtropCanon3.cxsmi -60: -60: Test -60: -60: BMS-986142_3d_chiral.cxsmi -60: -60: Test -60: -60: BMS-986142_3d.cxsmi -60: -60: =============================================================================== -60: All tests passed (2496 assertions in 31 test cases) -60: -161: file rxn_test1_2.png gave hash 3312211595U not the expected 507435337U -161: file rxn_test1_3.png gave hash 288594716U not the expected 1590809137U -161: file rxn_test1_4.png gave hash 1996676260U not the expected 1766700542U -160: file contourMol_1.svg gave hash 4125787245U not the expected 3634867913U -160: file contourMol_2.svg gave hash 4241964660U not the expected 1815941817U -160: file contourMol_3.svg gave hash 1333854566U not the expected 2579392727U -160: file contourMol_4.svg gave hash 4249475618U not the expected 2914799663U -130: [17:55:20] done -130: [17:55:20] ------------------------------------- -130: [17:55:20] Test Rooted Topological Torsions. -130: [17:55:20] done -130: [17:55:20] ------------------------------------- -130: [17:55:20] Test ignoring atoms in Topological Torsions. -130: [17:55:20] done -130: [17:55:20] ------------------------------------- -130: [17:55:20] ------------------------------------- -130: [17:55:20] Test Topological Torsions including info about chirality. -130: [17:55:20] done -130: [17:55:20] ------------------------------------- -130: [17:55:20] Test GitHub Issue 25: fingerprint backwards compatibility. -130: [17:55:20] done -130: [17:55:20] ------------------------------------- -130: [17:55:20] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. -130: [17:55:20] done -130: [17:55:20] ------------------------------------- -130: [17:55:20] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 -130: [17:55:20] done -130: [17:55:20] ------------------------------------- -130: [17:55:20] Test convenience and bulk fp calculation functions -125/236 Test #60: cxsmilesTest ........................... Passed 1.33 sec -126/236 Test #165: FMCStest ............................... Passed 0.08 sec -159: file test5_1.png gave hash 650561118U not the expected 571291290U +126/236 Test #165: FMCStest ............................... Passed 0.05 sec +test 166 + Start 166: molHashCatchTest + +166: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/molHashCatchTest +166: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolHash +166: Test timeout computed to be: 1500 +154: .[14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +161: file rxn_test1_6.png gave hash 1112775934U not the expected 3791582903U +148: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +117: =>start test 1 WHIM custom +117: [14:17:41] test on : 365 molecules done +147: [14:17:41] UFFTYPER: Unrecognized charge state for atom: 5 +159: generating reference drawings +161: file rxn_test1_7.png gave hash 1360101162U not the expected 1461397406U +148: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +161: file rxn_test1_7.svg gave hash 2324077060U not the expected 1831465890U +161: Done +161: ----------------- Test 2: some examples that caused problems in testing +108: .............[14:17:41] SMILES Parse Error: syntax error while parsing: --- +108: [14:17:41] SMILES Parse Error: check for mistakes around position 1: +108: [14:17:41] --- +108: [14:17:41] ^ +108: [14:17:41] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [14:17:41] dasfsadf +108: [14:17:41] SMILES Parse Error: syntax error while parsing: --- +108: [14:17:41] SMILES Parse Error: check for mistakes around position 1: +108: [14:17:41] --- +108: [14:17:41] ^ +108: [14:17:41] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [14:17:41] dasfsadf +108: [14:17:41] SMILES Parse Error: syntax error while parsing: --- +108: [14:17:41] SMILES Parse Error: check for mistakes around position 1: +108: [14:17:41] --- +108: [14:17:41] ^ +108: [14:17:41] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [14:17:41] dasfsadf +108: [14:17:41] SMILES Parse Error: syntax error while parsing: --- +108: [14:17:41] SMILES Parse Error: check for mistakes around position 1: +108: [14:17:41] --- +108: [14:17:41] ^ +108: [14:17:41] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [14:17:41] dasfsadf +108: [14:17:41] SMILES Parse Error: syntax error while parsing: --- +108: [14:17:41] SMILES Parse Error: check for mistakes around position 1: +108: [14:17:41] --- +108: [14:17:41] ^ +108: [14:17:41] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [14:17:41] dasfsadf +108: [14:17:41] SMILES Parse Error: syntax error while parsing: --- +108: [14:17:41] SMILES Parse Error: check for mistakes around position 1: +108: [14:17:41] --- +108: [14:17:41] ^ +108: [14:17:41] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [14:17:41] dasfsadf +108: [14:17:41] SMILES Parse Error: syntax error while parsing: --- +108: [14:17:41] SMILES Parse Error: check for mistakes around position 1: +108: [14:17:41] --- +108: [14:17:41] ^ +108: [14:17:41] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [14:17:41] dasfsadf +108: [14:17:41] SMILES Parse Error: syntax error while parsing: --- +108: [14:17:41] SMILES Parse Error: check for mistakes around position 1: +108: [14:17:41] --- +108: [14:17:41] ^ +108: [14:17:41] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [14:17:41] dasfsadf +108: [14:17:41] SMILES Parse Error: syntax error while parsing: --- +108: [14:17:41] SMILES Parse Error: check for mistakes around position 1: +108: [14:17:41] --- +108: [14:17:41] ^ +108: [14:17:41] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [14:17:41] dasfsadf +108: [14:17:41] SMILES Parse Error: syntax error while parsing: --- +108: [14:17:41] SMILES Parse Error: check for mistakes around position 1: +108: [14:17:41] --- +108: [14:17:41] ^ +108: [14:17:41] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [14:17:41] dasfsadf +108: [14:17:41] SMILES Parse Error: syntax error while parsing: --- +108: [14:17:41] SMILES Parse Error: check for mistakes around position 1: +108: [14:17:41] --- +108: [14:17:41] ^ +108: [14:17:41] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [14:17:41] dasfsadf +108: [14:17:41] SMILES Parse Error: syntax error while parsing: --- +108: [14:17:41] SMILES Parse Error: check for mistakes around position 1: +108: [14:17:41] --- +108: [14:17:41] ^ +108: [14:17:41] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [14:17:41] dasfsadf +108: [14:17:41] SMILES Parse Error: syntax error while parsing: --- +108: [14:17:41] SMILES Parse Error: check for mistakes around position 1: +108: [14:17:41] --- +108: [14:17:41] ^ +108: [14:17:41] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [14:17:41] dasfsadf +108: [14:17:41] SMILES Parse Error: syntax error while parsing: --- +108: [14:17:41] SMILES Parse Error: check for mistakes around position 1: +108: [14:17:41] --- +108: [14:17:41] ^ +108: [14:17:41] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [14:17:41] dasfsadf +108: [14:17:41] SMILES Parse Error: syntax error while parsing: --- +108: [14:17:41] SMILES Parse Error: check for mistakes around position 1: +108: [14:17:41] --- +108: [14:17:41] ^ +108: [14:17:41] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [14:17:41] dasfsadf +108: [14:17:41] SMILES Parse Error: syntax error while parsing: --- +108: [14:17:41] SMILES Parse Error: check for mistakes around position 1: +108: [14:17:41] --- +108: [14:17:41] ^ +108: [14:17:41] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [14:17:41] dasfsadf +108: [14:17:41] SMILES Parse Error: syntax error while parsing: --- +108: [14:17:41] SMILES Parse Error: check for mistakes around position 1: +108: [14:17:41] --- +108: [14:17:41] ^ +108: [14:17:41] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [14:17:41] dasfsadf +148: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +141: [14:17:41] Rep: 20 Mol:0 +108: [14:17:41] SMILES Parse Error: syntax error while parsing: --- +108: [14:17:41] SMILES Parse Error: check for mistakes around position 1: +108: [14:17:41] --- +108: [14:17:41] ^ +108: [14:17:41] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +141: [14:17:41] Rep: 20 Mol:4 +141: [14:17:41] Rep: 20 Mol:8 +141: [14:17:41] Rep: 20 Mol:12 +141: [14:17:41] Rep: 20 Mol:16 +108: [14:17:41] SMILES Parse Error: syntax error while parsing: --- +108: [14:17:41] SMILES Parse Error: check for mistakes around position 1: +108: [14:17:41] --- +108: [14:17:41] ^ +108: [14:17:41] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [14:17:41] dasfsadf +108: [14:17:41] SMILES Parse Error: syntax error while parsing: --- +108: [14:17:41] SMILES Parse Error: check for mistakes around position 1: +108: [14:17:41] --- +108: [14:17:41] ^ +108: [14:17:41] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [14:17:41] dasfsadf +108: [14:17:41] dasfsadf +108: [14:17:41] SMILES Parse Error: syntax error while parsing: --- +108: [14:17:41] SMILES Parse Error: check for mistakes around position 1: +108: [14:17:41] --- +108: [14:17:41] ^ +108: [14:17:41] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [14:17:41] dasfsadf +108: [14:17:41] SMILES Parse Error: syntax error while parsing: --- +108: [14:17:41] SMILES Parse Error: check for mistakes around position 1: +108: [14:17:41] --- +108: [14:17:41] ^ +108: [14:17:41] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [14:17:41] dasfsadf +108: [14:17:41] SMILES Parse Error: syntax error while parsing: --- +108: [14:17:41] SMILES Parse Error: check for mistakes around position 1: +108: [14:17:41] --- +108: [14:17:41] ^ +108: [14:17:41] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [14:17:41] dasfsadf +108: [14:17:41] SMILES Parse Error: syntax error while parsing: --- +108: [14:17:41] SMILES Parse Error: check for mistakes around position 1: +108: [14:17:41] --- +108: [14:17:41] ^ +108: [14:17:41] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [14:17:41] dasfsadf +108: [14:17:41] SMILES Parse Error: syntax error while parsing: --- +108: [14:17:41] SMILES Parse Error: check for mistakes around position 1: +108: [14:17:41] --- +108: [14:17:41] ^ +108: [14:17:41] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [14:17:41] dasfsadf +108: [14:17:41] SMILES Parse Error: syntax error while parsing: --- +108: [14:17:41] SMILES Parse Error: check for mistakes around position 1: +108: [14:17:41] --- +108: [14:17:41] ^ +108: [14:17:41] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [14:17:41] dasfsadf +108: [14:17:41] SMILES Parse Error: syntax error while parsing: --- +108: [14:17:41] SMILES Parse Error: check for mistakes around position 1: +108: [14:17:41] --- +108: [14:17:41] ^ +108: [14:17:41] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [14:17:41] dasfsadf +141: [14:17:41] Rep: 20 Mol:20 +141: [14:17:41] Rep: 20 Mol:24 +141: [14:17:41] Rep: 20 Mol:28 +108: [14:17:41] SMILES Parse Error: syntax error while parsing: --- +108: [14:17:41] SMILES Parse Error: check for mistakes around position 1: +108: [14:17:41] --- +108: [14:17:41] ^ +108: [14:17:41] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [14:17:41] dasfsadf +108: [14:17:41] SMILES Parse Error: syntax error while parsing: --- +108: [14:17:41] SMILES Parse Error: check for mistakes around position 1: +108: [14:17:41] --- +108: [14:17:41] ^ +108: [14:17:41] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [14:17:41] dasfsadf +108: [14:17:41] SMILES Parse Error: syntax error while parsing: --- +108: [14:17:41] SMILES Parse Error: check for mistakes around position 1: +108: [14:17:41] --- +108: [14:17:41] ^ +108: [14:17:41] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [14:17:41] dasfsadf +148: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +166: Randomness seeded to: 3336208695 +166: =============================================================================== +166: All tests passed (363 assertions in 14 test cases) +166: +127/236 Test #166: molHashCatchTest ....................... Passed 0.18 sec test 167 Start 167: pyMolHash 167: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolHash/Wrap/testMolHash.py" 167: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/Wrap 167: Test timeout computed to be: 1500 +141: [14:17:41] Rep: 20 Mol:3 +141: [14:17:41] Rep: 20 Mol:7 +141: [14:17:41] Rep: 20 Mol:11 +141: [14:17:41] Rep: 20 Mol:15 +141: [14:17:41] Rep: 20 Mol:19 +141: [14:17:41] Rep: 20 Mol:23 +141: [14:17:41] Rep: 20 Mol:27 +161: file rxn_test2_1.png gave hash 3339775168U not the expected 3551633840U +148: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +141: [14:17:41] Rep: 20 Mol:31 +128/236 Test #127: pyMolDescriptors3D ..................... Passed 2.57 sec test 168 Start 168: testMMPA 168: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/testMMPA 168: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MMPA 168: Test timeout computed to be: 1500 -159: file test5_2.png gave hash 2649140411U not the expected 97265124U -160: file contourMol_5.svg gave hash 3954963517U not the expected 3792684719U -147: [17:55:20] UFFTYPER: Unrecognized charge state for atom: 5 -147: [17:55:20] UFFTYPER: Unrecognized charge state for atom: 5 -161: file rxn_test1_5.png gave hash 1068409486U not the expected 2552100594U -69: ---------------------------------- -69: ---------------------------------- -143: processing -143: launch :0 -143: launch :1 -143: launch :2 -143: [17:55:20] Rep: launch :3[17:55:20] Rep: 0 Mol:1 -143: 0 Mol:0 -143: [17:55:20] Rep: 0 Mol:5 -159: file test5_3.png gave hash 2951986966U not the expected 606188176U -143: [17:55:20] Rep: 0 Mol:9 -159: Done -159: ----------------- Test 6 (atom labels) -145: ... -145: ---------------------------------------------------------------------- -145: Ran 19 tests in 0.173s -145: -145: OK -143: -143: [17:55:20] Rep: 0 Mol:2 -69: [17:55:20] -69: -69: **** -69: Pre-condition Violation -69: rlabel out of range for MDL files -69: Violation occurred on line 863 in file ./Code/GraphMol/Atom.cpp -69: Failed Expression: rlabel >= 0 && rlabel < 100 -69: ---------- -69: Stacktrace: -69: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -69: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -69: 2# RDKit::setAtomRLabel(RDKit::Atom*, int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -69: 3# 0x000055BED1236FFF in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 4# 0x000055BED12903EA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 5# 0x000055BED1210923 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 6# 0x00007FCE1EA33CA8 in /lib/x86_64-linux-gnu/libc.so.6 -69: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -69: 8# 0x000055BED1210AD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: ---------- -69: **** -69: -143: [17:55:20] Rep: 0 Mol:3 -69: [17:55:20] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -147: [17:55:20] UFFTYPER: Unrecognized charge state for atom: 5 -143: [17:55:20] Rep: 0 Mol:13 -159: Done -159: ----------------- Test 7 (backgrounds) -143: [17:55:20] Rep: 0 Mol:17 -143: [17:55:20] Rep: 0 Mol:4 -159: file test7_1.png gave hash 2406197059U not the expected 1322246680U -161: file rxn_test1_6.png gave hash 1112775934U not the expected 3791582903U -159: file test7_2.png gave hash 4033628357U not the expected 1499012715U -159: Done -159: ----------------- Test8: PrepareMolDrawing -159: Done -159: ----------------- Test multi-threaded drawing -159: reading molecules -143: [17:55:20] Rep: 0 Mol:21 -108: .............[17:55:20] SMILES Parse Error: syntax error while parsing: --- -108: [17:55:20] SMILES Parse Error: check for mistakes around position 1: -108: [17:55:20] --- -108: [17:55:20] ^ -108: [17:55:20] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [17:55:20] dasfsadf -108: [17:55:20] SMILES Parse Error: syntax error while parsing: --- -108: [17:55:20] SMILES Parse Error: check for mistakes around position 1: -108: [17:55:20] --- -108: [17:55:20] ^ -108: [17:55:20] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [17:55:20] dasfsadf -108: [17:55:20] SMILES Parse Error: syntax error while parsing: --- -108: [17:55:20] SMILES Parse Error: check for mistakes around position 1: -108: [17:55:20] --- -108: [17:55:20] ^ -108: [17:55:20] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [17:55:20] dasfsadf -108: [17:55:20] SMILES Parse Error: syntax error while parsing: --- -108: [17:55:20] SMILES Parse Error: check for mistakes around position 1: -108: [17:55:20] --- -108: [17:55:20] ^ -108: [17:55:20] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [17:55:20] dasfsadf -108: [17:55:20] SMILES Parse Error: syntax error while parsing: --- -108: [17:55:20] SMILES Parse Error: check for mistakes around position 1: -108: [17:55:20] --- -108: [17:55:20] ^ -108: [17:55:20] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [17:55:20] dasfsadf -108: [17:55:20] SMILES Parse Error: syntax error while parsing: --- -108: [17:55:20] SMILES Parse Error: check for mistakes around position 1: -108: [17:55:20] --- -108: [17:55:20] ^ -108: [17:55:20] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [17:55:20] dasfsadf -143: [17:55:20] Rep: 0 Mol:7 -143: [17:55:20] Rep: 0 Mol:25 -143: [17:55:20] Rep: 0 Mol:11 -108: [17:55:20] SMILES Parse Error: syntax error while parsing: --- -108: [17:55:20] SMILES Parse Error: check for mistakes around position 1: -108: [17:55:20] --- -108: [17:55:20] ^ -108: [17:55:20] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [17:55:20] dasfsadf -108: [17:55:20] SMILES Parse Error: syntax error while parsing: --- -108: [17:55:20] SMILES Parse Error: check for mistakes around position 1: -108: [17:55:20] --- -108: [17:55:20] ^ -108: [17:55:20] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [17:55:20] dasfsadf -108: [17:55:20] SMILES Parse Error: syntax error while parsing: --- -108: [17:55:20] SMILES Parse Error: check for mistakes around position 1: -108: [17:55:20] --- -108: [17:55:20] ^ -108: [17:55:20] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [17:55:20] dasfsadf -108: [17:55:20] SMILES Parse Error: syntax error while parsing: --- -108: [17:55:20] SMILES Parse Error: check for mistakes around position 1: -108: [17:55:20] --- -108: [17:55:20] ^ -108: [17:55:20] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [17:55:20] dasfsadf -108: [17:55:20] SMILES Parse Error: syntax error while parsing: --- -108: [17:55:20] SMILES Parse Error: check for mistakes around position 1: -108: [17:55:20] --- -108: [17:55:20] ^ -108: [17:55:20] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [17:55:20] dasfsadf -108: [17:55:20] SMILES Parse Error: syntax error while parsing: --- -108: [17:55:20] SMILES Parse Error: check for mistakes around position 1: -108: [17:55:20] --- -108: [17:55:20] ^ -108: [17:55:20] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [17:55:20] dasfsadf -108: [17:55:20] SMILES Parse Error: syntax error while parsing: --- -108: [17:55:20] SMILES Parse Error: check for mistakes around position 1: -108: [17:55:20] --- -108: [17:55:20] ^ -108: [17:55:20] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [17:55:20] dasfsadf -108: [17:55:20] SMILES Parse Error: syntax error while parsing: --- -108: [17:55:20] SMILES Parse Error: check for mistakes around position 1: -108: [17:55:20] --- -108: [17:55:20] ^ -108: [17:55:20] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [17:55:20] dasfsadf -108: [17:55:20] SMILES Parse Error: syntax error while parsing: --- -108: [17:55:20] SMILES Parse Error: check for mistakes around position 1: -108: [17:55:20] --- -108: [17:55:20] ^ -108: [17:55:20] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [17:55:20] dasfsadf -108: [17:55:20] SMILES Parse Error: syntax error while parsing: --- -143: [17:55:20] Rep: 0 Mol:15 -108: [17:55:20] SMILES Parse Error: check for mistakes around position 1: -108: [17:55:20] --- -108: [17:55:20] ^ -108: [17:55:20] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [17:55:20] dasfsadf -108: [17:55:20] SMILES Parse Error: syntax error while parsing: --- -108: [17:55:20] SMILES Parse Error: check for mistakes around position 1: -108: [17:55:20] --- -108: [17:55:20] ^ -143: [17:55:20] Rep: 0 Mol:19 -143: [17:55:20] Rep: 0 Mol:29 -143: [17:55:20] Rep: 0 Mol:6 -143: [17:55:20] Rep: 0 Mol:23 +154: ..[14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +154: .[14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +154: .[14:17:41] SMARTS Parse Error: syntax error while parsing: [N,O;!HQ] +154: [14:17:41] SMARTS Parse Error: Failed parsing SMARTS '[N,O;!HQ]' for input: '[N,O;!HQ]' +154: ... +154: ---------------------------------------------------------------------- +154: Ran 9 tests in 0.299s +154: +154: OK +148: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +161: 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 +160: file testGithub3226_1.png gave hash 2093087177U not the expected 3165135374U +148: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() 168: 168: TEST mol: Case1 Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1 Case1 -168: Time elapsed 0.005148 seconds +168: Time elapsed 0.004974 seconds 168: 1: res= NULL,C[*:1].C[C:2](C(=O)Nc1ccccc1[*:1])[NH+]1CCCC1 168: 1: NOREF. Reference data NOT LISTED in test case. +141: [14:17:41] Rep: 40 Mol:1 +141: [14:17:41] Rep: 40 Mol:5 +141: [14:17:41] Rep: 40 Mol:9 +141: [14:17:41] Rep: 40 Mol:13 +89: [14:17:41] Explicit valence for atom # 9 N, 5, is greater than permitted 168: 2: res= c1ccc([*:2])c([*:1])c1,C[*:1].C[C:3](C(=O)N[*:2])[NH+]1CCCC1 168: 2: NOREF. Reference data NOT LISTED in test case. 168: 3: res= O=C(Nc1ccccc1[*:1])[*:2],C[*:1].C[C:3]([NH+]1CCCC1)[*:2] @@ -28433,107 +28326,19 @@ 168: 4: NOREF. Reference data NOT LISTED in test case. 168: 5: res= O=C(Nc1ccccc1[*:1])[C:0]([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:1].C[*:2] 168: 5: NOREF. Reference data NOT LISTED in test case. -166: Randomness seeded to: 2815000804 -166: =============================================================================== -166: All tests passed (363 assertions in 14 test cases) -166: -108: [17:55:20] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [17:55:20] dasfsadf -108: [17:55:20] SMILES Parse Error: syntax error while parsing: --- -108: [17:55:20] SMILES Parse Error: check for mistakes around position 1: -108: [17:55:20] --- -108: [17:55:20] ^ -108: [17:55:20] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [17:55:20] dasfsadf -108: [17:55:20] SMILES Parse Error: syntax error while parsing: --- -108: [17:55:20] SMILES Parse Error: check for mistakes around position 1: -108: [17:55:20] --- -108: [17:55:20] ^ -108: [17:55:20] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [17:55:20] dasfsadf -127/236 Test #166: molHashCatchTest ....................... Passed 0.12 sec -143: [17:55:20] Rep: 0 Mol:27 -108: [17:55:20] SMILES Parse Error: syntax error while parsing: --- -108: [17:55:20] SMILES Parse Error: check for mistakes around position 1: -108: [17:55:20] --- -108: [17:55:20] ^ -108: [17:55:20] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [17:55:20] dasfsadf 168: 6: res= C[C:0](C(=O)Nc1ccccc1[*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1] 168: 6: NOREF. Reference data NOT LISTED in test case. -test 169 - Start 169: pyMMPA - -169: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MMPA/Wrap/testMMPA.py" -169: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/Wrap -169: Test timeout computed to be: 1500 -143: [17:55:20] Rep: 0 Mol:31 -108: [17:55:20] SMILES Parse Error: syntax error while parsing: --- -108: [17:55:20] SMILES Parse Error: check for mistakes around position 1: -108: [17:55:20] --- -108: [17:55:20] ^ -108: [17:55:20] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [17:55:20] dasfsadf -108: [17:55:20] SMILES Parse Error: syntax error while parsing: --- -108: [17:55:20] SMILES Parse Error: check for mistakes around position 1: -108: [17:55:20] --- -108: [17:55:20] ^ -108: [17:55:20] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [17:55:20] dasfsadf -108: [17:55:20] SMILES Parse Error: syntax error while parsing: --- -108: [17:55:20] SMILES Parse Error: check for mistakes around position 1: -108: [17:55:20] --- -108: [17:55:20] ^ -108: [17:55:20] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [17:55:20] dasfsadf -108: [17:55:20] SMILES Parse Error: syntax error while parsing: --- -108: [17:55:20] SMILES Parse Error: check for mistakes around position 1: -108: [17:55:20] --- -108: [17:55:20] ^ -108: [17:55:20] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [17:55:20] dasfsadf -108: [17:55:20] SMILES Parse Error: syntax error while parsing: --- -108: [17:55:20] SMILES Parse Error: check for mistakes around position 1: -108: [17:55:20] --- -108: [17:55:20] ^ -108: [17:55:20] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [17:55:20] dasfsadf -108: [17:55:20] SMILES Parse Error: syntax error while parsing: --- -108: [17:55:20] SMILES Parse Error: check for mistakes around position 1: -108: [17:55:20] --- -108: [17:55:20] ^ -108: [17:55:20] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [17:55:20] dasfsadf -108: [17:55:20] SMILES Parse Error: syntax error while parsing: --- -108: [17:55:20] SMILES Parse Error: check for mistakes around position 1: -108: [17:55:20] --- -108: [17:55:20] ^ -108: [17:55:20] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [17:55:20] dasfsadf -108: [17:55:20] SMILES Parse Error: syntax error while parsing: --- -108: [17:55:20] SMILES Parse Error: check for mistakes around position 1: -108: [17:55:20] --- -108: [17:55:20] ^ -108: [17:55:20] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [17:55:20] dasfsadf -108: [17:55:20] SMILES Parse Error: syntax error while parsing: --- -108: [17:55:20] SMILES Parse Error: check for mistakes around position 1: -108: [17:55:20] --- -108: [17:55:20] ^ -108: [17:55:20] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [17:55:20] dasfsadf -108: [17:55:20] SMILES Parse Error: syntax error while parsing: --- -108: [17:55:20] SMILES Parse Error: check for mistakes around position 1: -108: [17:55:20] --- -108: [17:55:20] ^ -108: [17:55:20] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [17:55:20] dasfsadf 168: 7: res= NULL,C[C:2](C(=O)N[*:1])[NH+]1CCCC1.Cc1ccccc1[*:1] 168: 7: NOREF. Reference data NOT LISTED in test case. 168: 8: res= O=C(N[*:3])[*:1],C[C:2]([NH+]1CCCC1)[*:1].Cc1ccccc1[*:3] 168: 8: NOREF. Reference data NOT LISTED in test case. 168: 9: res= O=C(N[*:2])[C:0]([NH+]1CCCC1)[*:1],C[*:1].Cc1ccccc1[*:2] 168: 9: NOREF. Reference data NOT LISTED in test case. +147: [14:17:41] UFFTYPER: Unrecognized charge state for atom: 6 +141: [14:17:41] Rep: 40 Mol:17 +141: [14:17:41] Rep: 40 Mol:21 +141: [14:17:41] Rep: 40 Mol:25 +141: [14:17:41] Rep: 40 Mol:29 168: 10: res= O=C(N[*:3])[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1].Cc1ccccc1[*:3] 168: 10: NOREF. Reference data NOT LISTED in test case. 168: 11: res= C[C:0](C(=O)N[*:2])[*:1],C1CC[NH+]([*:1])C1.Cc1ccccc1[*:2] @@ -28544,6 +28349,9 @@ 168: 13: NOREF. Reference data NOT LISTED in test case. 168: 14: res= [C:0]([*:1])([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:1].Cc1ccccc1NC(=O)[*:2] 168: 14: NOREF. Reference data NOT LISTED in test case. +161: file rxn_test2_2_1.png gave hash 457778262U not the expected 1268122583U +148: [14:17:41] Molecule does not have explicit Hs. Consider calling AddHs() +147: [14:17:41] UFFTYPER: Unrecognized charge state for atom: 6 168: 15: res= C[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.Cc1ccccc1NC(=O)[*:1] 168: 15: NOREF. Reference data NOT LISTED in test case. 168: 16: res= NULL,C[*:1].Cc1ccccc1NC(=O)[C:2]([NH+]1CCCC1)[*:1] @@ -28552,35 +28360,30 @@ 168: 17: NOREF. Reference data NOT LISTED in test case. 168: 18: res= NULL,C1CC[NH+]([*:1])C1.Cc1ccccc1NC(=O)[C:2](C)[*:1] 168: 18: NOREF. Reference data NOT LISTED in test case. -143: [17:55:20] Rep: 0 Mol:8 -143: [17:55:20] Rep: 0 Mol:10 -127: ........ -127: ---------------------------------------------------------------------- -127: Ran 8 tests in 0.221s -127: -127: OK -159: generating reference drawings -154: .[17:55:20] Molecule does not have explicit Hs. Consider calling AddHs() -143: [17:55:20] Rep: 0 Mol:12 -161: file rxn_test1_7.png gave hash 1360101162U not the expected 1461397406U -128/236 Test #145: pyForceFieldHelpers .................... Passed 0.53 sec -test 170 - Start 170: testRascalMCES +108: .[14:17:42] SMILES Parse Error: syntax error while parsing: mydoghasfleas +108: [14:17:42] SMILES Parse Error: check for mistakes around position 1: +108: [14:17:42] mydoghasfleas +108: [14:17:42] ^ +108: [14:17:42] SMILES Parse Error: Failed parsing SMILES 'mydoghasfleas' for input: 'mydoghasfleas' +159: processing +159: launch :0 +160: file testGithub3226_2.png gave hash 228776032U not the expected 643975155U +129/236 Test #154: pyChemicalFeatures ..................... Passed 1.22 sec +test 169 + Start 169: pyMMPA -170: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES/testRascalMCES -170: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES -170: Test timeout computed to be: 1500 -125: Warning: Atom Count for residue ASN39A does not match expected count -143: [17:55:20] Rep: 0 Mol:16 -161: file rxn_test1_7.svg gave hash 2324077060U not the expected 1831465890U -143: [17:55:20] Rep: 0 Mol:20 -161: Done -161: ----------------- Test 2: some examples that caused problems in testing +169: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MMPA/Wrap/testMMPA.py" +169: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/Wrap +169: Test timeout computed to be: 1500 +161: 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 +159: launch :1 +159: launch :2 +159: launch :3 168: 168: --- UNMATCHED Reference RESULTS: --- 168: 1: Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1,Case1,[*:1][C:7]([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:2].Cc1ccccc1NC(=O)[*:1] 168: ----------------------------------- -168: Time elapsed 0.004414 seconds +168: Time elapsed 0.012562 seconds 168: 168: TEST 1 mol: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-] ZINC21984717 168: 1: NULL, C[*:1].O=C(NCCO)c1c([*:1])n([O-])c2ccccc2[n+]1=O @@ -28589,32 +28392,90 @@ 168: 2: PASSED. matchedRefRes = 1 168: 3: O=C(N[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O, C[*:1].OCC[*:2] 168: 3: PASSED. matchedRefRes = 6 -158: . -158: ---------------------------------------------------------------------- -158: Ran 1 test in 0.010s -158: -158: OK 168: 4: O=C(NC[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O, C[*:1].OC[*:2] 168: 4: PASSED. matchedRefRes = 13 168: 5: O=C(NCC[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O, C[*:1].O[*:2] 168: 5: PASSED. matchedRefRes = 12 +161: file rxn_test2_2_2.png gave hash 4285088210U not the expected 82821108U +148: [14:17:42] Molecule does not have explicit Hs. Consider calling AddHs() +68: Test +68: +68: FalseAtropisomer.mrv +68: +68: Test +68: +68: AtropEnhancedStereo.mrv +68: +68: Test +68: +68: AtropManyChirals.mrv +68: +68: Test +68: +68: AtropManyChiralsEnhanced.mrv +68: +68: Test +68: +68: AtropManyChiralsEnhanced2.mrv +68: +68: Test +68: +68: AtropManyChiralsEnhanced3.mrv +68: +68: Test +68: +68: AtropManyChiralsEnhanced4.mrv +68: +68: Test +68: +68: BMS-986142_3d_chiral.mrv +68: +68: Test +68: +68: BMS-986142_3d.mrv +68: +68: Test +68: +68: BMS-986142_atrop1.mrv +68: +68: Test +68: +68: BMS-986142_atrop2.mrv +68: +68: Test +68: +68: BMS-986142_atrop3.mrv +68: +68: Test +68: +68: BMS-986142_atrop4.mrv +68: +68: Test +68: +68: BMS-986142_atrop5.mrv +68: +68: [14:17:42] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +68: [14:17:42] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +160: file testGithub3226_3.png gave hash 1938488947U not the expected 3119571946U 168: 6: NULL, Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].O=C(NCCO)[*:1] 168: 6: PASSED. matchedRefRes = 10 -148: .[17:55:20] Molecule does not have explicit Hs. Consider calling AddHs() -143: [17:55:20] Rep: 0 Mol:24 168: 7: O=C(N[*:1])[*:2], Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OCC[*:1] 168: 7: NOREF. Reference data NOT LISTED in test case.O=C(N[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OCC[*:1] 168: 8: O=C(NC[*:1])[*:2], Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] 168: 8: NOREF. Reference data NOT LISTED in test case.O=C(NC[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] 168: 9: O=C(NCC[*:1])[*:2], Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].O[*:1] 168: 9: NOREF. Reference data NOT LISTED in test case.O=C(NCC[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].O[*:1] -154: .[17:55:20] Molecule does not have explicit Hs. Consider calling AddHs() 168: 10: NULL, Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].OCC[*:1] 168: 10: PASSED. matchedRefRes = 3 -147: [17:55:20] UFFTYPER: Unrecognized charge state for atom: 6 +141: [14:17:42] Rep: 20 Mol:2 +141: [14:17:42] Rep: 20 Mol:6 +141: [14:17:42] Rep: 20 Mol:10 +147: [14:17:42] UFFTYPER: Unrecognized charge state for atom: 6 +161: 2 Cc1c(cc([nH]1)[c:1]2[cH:2][cH:3][cH:4][cH:5][cH:6]2)[C:7](=[O:8])[NH:9][CH2:10][CH2:11]>>CCc1nc(c(n1[c:1]2[cH:2][cH:3][cH:4][cH:5][cH:6]2)C)[C:7](=[O:8])[NH:9][CH2:10][CH2:11] Cc1c(cc([nH]1)c2ccccc2)C(=O)NCCN3CCN(C +161: 2 C3)c4cccc(c4Cl)Cl CCc1nc(c(n1c2ccccc2)C)C(=O)NCCN3CCN(CC3)c4cccc(c4Cl)Cl +161: 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 168: 11: C([*:1])[*:2], Cc1c(C(=O)N[*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] 168: 11: NOREF. Reference data NOT LISTED in test case.C([*:1])[*:2],Cc1c(C(=O)N[*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] -143: [17:55:20] Rep: 0 Mol:28 168: 12: C(C[*:2])[*:1], Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].O[*:2] 168: 12: PASSED. matchedRefRes = 8 168: 13: NULL, Cc1c(C(=O)NC[*:1])[n+](=O)c2ccccc2n1[O-].OC[*:1] @@ -28623,9 +28484,11 @@ 168: 14: PASSED. matchedRefRes = 11 168: 15: NULL, Cc1c(C(=O)NCC[*:1])[n+](=O)c2ccccc2n1[O-].O[*:1] 168: 15: PASSED. matchedRefRes = 2 -143: [17:55:20] Rep: 0 Mol:14 -147: [17:55:20] UFFTYPER: Unrecognized charge state for atom: 6 -143: [17:55:20] Rep: 0 Mol:18 +141: [14:17:42] Rep: 20 Mol:14 +141: [14:17:42] Rep: 20 Mol:18 +141: [14:17:42] Rep: 20 Mol:22 +141: [14:17:42] Rep: 20 Mol:26 +141: [14:17:42] Rep: 20 Mol:30 168: 168: --- UNMATCHED Reference RESULTS: --- 168: 5: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,C([*:1])[*:2],Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].OC[*:2] @@ -28635,12 +28498,13 @@ 168: ----------------------------------- 168: 168: TEST mol: ZINC21984717 Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-] ZINC21984717 -168: Time elapsed 0.004421 seconds +168: Time elapsed 0.008788 seconds 168: 1: res= NULL,C[*:1].O=C(NCCO)c1c([*:1])n([O-])c2ccccc2[n+]1=O 168: 1: PASSED. matchedRefRes = 4 168: 2: res= O=[n+]1c([*:2])c([*:1])n([O-])c2ccccc21,C[*:1].O=C(NCCO)[*:2] 168: 2: PASSED. matchedRefRes = 1 -143: [17:55:20] Rep: 0 Mol:22 +148: [14:17:42] Molecule does not have explicit Hs. Consider calling AddHs() +125: Warning: Atom Count for residue GLU53A does not match expected count 168: 3: res= O=C(N[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O,C[*:1].OCC[*:2] 168: 3: PASSED. matchedRefRes = 6 168: 4: res= O=C(NC[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O,C[*:1].OC[*:2] @@ -28649,7 +28513,6 @@ 168: 5: PASSED. matchedRefRes = 12 168: 6: res= NULL,Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].O=C(NCCO)[*:1] 168: 6: PASSED. matchedRefRes = 10 -143: [17:55:20] Rep: 0 Mol:26 168: 7: res= O=C(N[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OCC[*:1] 168: 7: NOREF. Reference data NOT LISTED in test case. 168: 8: res= O=C(NC[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] @@ -28658,7 +28521,17 @@ 168: 9: NOREF. Reference data NOT LISTED in test case. 168: 10: res= NULL,Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].OCC[*:1] 168: 10: PASSED. matchedRefRes = 3 -147: [17:55:20] UFFTYPER: Unrecognized charge state for atom: 6 +160: file testPNGMetadata_1.png gave hash 3033029091U not the expected 997629701U +126: Warning: Atom Count for residue ASN39A does not match expected count +141: [14:17:42] Rep: 40 Mol:3 +161: file rxn_test2_2_3.png gave hash 660865433U not the expected 3828365604U +141: [14:17:42] Rep: 40 Mol:7 +141: [14:17:42] Rep: 40 Mol:11 +141: [14:17:42] Rep: 40 Mol:15 +141: [14:17:42] Rep: 40 Mol:19 +141: [14:17:42] Rep: 40 Mol:23 +141: [14:17:42] Rep: 40 Mol:27 +141: [14:17:42] Rep: 40 Mol:31 168: 11: res= C([*:1])[*:2],Cc1c(C(=O)N[*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] 168: 11: NOREF. Reference data NOT LISTED in test case. 168: 12: res= C(C[*:2])[*:1],Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].O[*:2] @@ -28667,9 +28540,12 @@ 168: 13: PASSED. matchedRefRes = 9 168: 14: res= C([*:1])[*:2],Cc1c(C(=O)NC[*:1])[n+](=O)c2ccccc2n1[O-].O[*:2] 168: 14: PASSED. matchedRefRes = 11 +148: [14:17:42] Molecule does not have explicit Hs. Consider calling AddHs() +141: [14:17:42] Rep: 40 Mol:0 +141: [14:17:42] Rep: 40 Mol:4 168: 15: res= NULL,Cc1c(C(=O)NCC[*:1])[n+](=O)c2ccccc2n1[O-].O[*:1] 168: 15: PASSED. matchedRefRes = 2 -161: file rxn_test2_1.png gave hash 3339775168U not the expected 3551633840U +141: [14:17:42] Rep: 40 Mol:8 168: 168: --- UNMATCHED Reference RESULTS: --- 168: 5: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,C([*:1])[*:2],Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].OC[*:2] @@ -28679,19 +28555,11 @@ 168: ----------------------------------- 168: 168: TEST mol: Case1-SIMPLE CC(N1CC1)C(=O) Case1-SIMPLE -168: Time elapsed 0.001153 seconds +168: Time elapsed 0.001069 seconds 168: 1: res= NULL,C[*:1].O=CC(N1CC1)[*:1] 168: 1: PASSED. matchedRefRes = 2 -129/236 Test #127: pyMolDescriptors3D ..................... Passed 0.83 sec -143: [17:55:20] Rep: 0 Mol:30 168: 2: res= O=CC([*:1])[*:2],C1CN1[*:2].C[*:1] 168: 2: PASSED. matchedRefRes = 3 -test 171 - Start 171: testRascalCluster - -171: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES/testRascalCluster -171: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES -171: Test timeout computed to be: 1500 168: 3: res= C([*:1])([*:2])[*:3],C1CN1[*:3].C[*:1].O=C[*:2] 168: 3: NOREF. Reference data NOT LISTED in test case. 168: 4: res= C1CN1C([*:1])[*:2],C[*:1].O=C[*:2] @@ -28702,8 +28570,6 @@ 168: 6: NOREF. Reference data NOT LISTED in test case. 168: 7: res= NULL,CC(N1CC1)[*:1].O=C[*:1] 168: 7: PASSED. matchedRefRes = 7 -89: [17:55:20] Explicit valence for atom # 2 O, 4, is greater than permitted -160: file testGithub3226_1.png gave hash 2093087177U not the expected 3165135374U 168: 168: --- UNMATCHED Reference RESULTS: --- 168: 1: CC(N1CC1)C(=O),Case1-SIMPLE,C([*:1])([*:2])[*:3],C1CN1[*:2].C[*:1].O=C[*:3] @@ -28711,22 +28577,21 @@ 168: ----------------------------------- 168: 168: TEST mol: Case1 Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1 Case1 -168: Time elapsed 0.004980 seconds +168: Time elapsed 0.005121 seconds 168: 1: res= NULL,C[*:1].C[C:2](C(=O)Nc1ccccc1[*:1])[NH+]1CCCC1 168: 1: NOREF. Reference data NOT LISTED in test case. -130/236 Test #158: pyMolCatalog ........................... Passed 0.33 sec -test 172 - Start 172: pyRascalMCES - -172: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/Wrap/testRascalMCES.py" -172: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES/Wrap -172: Test timeout computed to be: 1500 168: 2: res= c1ccc([*:2])c([*:1])c1,C[*:1].C[C:3](C(=O)N[*:2])[NH+]1CCCC1 168: 2: NOREF. Reference data NOT LISTED in test case. 168: 3: res= O=C(Nc1ccccc1[*:1])[*:2],C[*:1].C[C:3]([NH+]1CCCC1)[*:2] 168: 3: NOREF. Reference data NOT LISTED in test case. 168: 4: res= O=C(Nc1ccccc1[*:1])[C:0]([NH+]1CCCC1)[*:2],C[*:1].C[*:2] 168: 4: NOREF. Reference data NOT LISTED in test case. +161: 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 +141: [14:17:42] Rep: 40 Mol:12 +141: [14:17:42] Rep: 40 Mol:16 +141: [14:17:42] Rep: 40 Mol:20 +141: [14:17:42] Rep: 40 Mol:24 +141: [14:17:42] Rep: 40 Mol:28 168: 5: res= O=C(Nc1ccccc1[*:1])[C:0]([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:1].C[*:2] 168: 5: NOREF. Reference data NOT LISTED in test case. 168: 6: res= C[C:0](C(=O)Nc1ccccc1[*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1] @@ -28737,19 +28602,18 @@ 168: 8: NOREF. Reference data NOT LISTED in test case. 168: 9: res= O=C(N[*:2])[C:0]([NH+]1CCCC1)[*:1],C[*:1].Cc1ccccc1[*:2] 168: 9: NOREF. Reference data NOT LISTED in test case. +69: [14:17:42] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +69: [14:17:42] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 168: 10: res= O=C(N[*:3])[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1].Cc1ccccc1[*:3] 168: 10: NOREF. Reference data NOT LISTED in test case. 168: 11: res= C[C:0](C(=O)N[*:2])[*:1],C1CC[NH+]([*:1])C1.Cc1ccccc1[*:2] 168: 11: NOREF. Reference data NOT LISTED in test case. -89: [17:55:20] Explicit valence for atom # 3 Be, 4, is greater than permitted -89: [17:55:20] Explicit valence for atom # 3 Al, 6, is greater than permitted 168: 12: res= NULL,C[C:2]([NH+]1CCCC1)[*:1].Cc1ccccc1NC(=O)[*:1] 168: 12: NOREF. Reference data NOT LISTED in test case. 168: 13: res= C1CC[NH+]([C:0]([*:1])[*:2])C1,C[*:1].Cc1ccccc1NC(=O)[*:2] 168: 13: NOREF. Reference data NOT LISTED in test case. 168: 14: res= [C:0]([*:1])([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:1].Cc1ccccc1NC(=O)[*:2] 168: 14: NOREF. Reference data NOT LISTED in test case. -160: file testGithub3226_2.png gave hash 228776032U not the expected 643975155U 168: 15: res= C[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.Cc1ccccc1NC(=O)[*:1] 168: 15: NOREF. Reference data NOT LISTED in test case. 168: 16: res= NULL,C[*:1].Cc1ccccc1NC(=O)[C:2]([NH+]1CCCC1)[*:1] @@ -28758,28 +28622,58 @@ 168: 17: NOREF. Reference data NOT LISTED in test case. 168: 18: res= NULL,C1CC[NH+]([*:1])C1.Cc1ccccc1NC(=O)[C:2](C)[*:1] 168: 18: NOREF. Reference data NOT LISTED in test case. -141: processing -141: launch :0 -141: launch :1 -141: launch :2 -141: launch :3 -141: [17:55:20] Rep: 0 Mol:2 -141: [17:55:20] Rep: 0 Mol:3 +68: Test +68: +68: BMS-986142_atrop6.mrv +68: +68: Test +68: +68: BMS-986142_atrop7.mrv +68: +68: Test +68: +68: BMS-986142_atrop8.mrv +68: +68: [14:17:42] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +68: [14:17:42] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +148: .[14:17:42] Molecule does not have explicit Hs. Consider calling AddHs() +160: file testPNGMetadata_2.png gave hash 2637596984U not the expected 1797853056U +161: file rxn_test2_2_4.png gave hash 1904681261U not the expected 1230108677U +108: ....... +108: ---------------------------------------------------------------------- +108: Ran 21 tests in 2.944s +108: +108: OK +108: (Five aromatic carbons And (Not any of Five aromatic carbons)) +108: (Five aromatic carbons Or (Not any of Five aromatic carbons)) +108: (Not (Five aromatic carbons And (Not any of Five aromatic carbons))) +108: ******************************************** +108: Testing: PAINS_A 2 +108: ******************************************** +108: Testing: PAINS_B 4 +108: ******************************************** +108: Testing: PAINS_C 8 +108: ******************************************** +108: Testing: PAINS 14 +108: (Not FilterMatcher) +108: Bar +108: Count 1 +108: ******************************************** +108: {'Cl,Br,I'} +108: 1 +108: 2 +108: running 168: 168: --- UNMATCHED Reference RESULTS: --- 168: 1: Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1,Case1,[*:1][C:7]([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:2].Cc1ccccc1NC(=O)[*:1] 168: ----------------------------------- 168: 168: TEST mol: Case2 O=C(OCc1ccccc1)C(O)c1ccccc1 Case2 -168: Time elapsed 0.005411 seconds +168: Time elapsed 0.017859 seconds 168: 1: res= NULL,O=C(O[*:1])C(O)c1ccccc1.c1ccc(C[*:1])cc1 168: 1: NOREF. Reference data NOT LISTED in test case. 168: 2: res= C([*:1])[*:2],O=C(O[*:1])C(O)c1ccccc1.c1ccc([*:2])cc1 168: 2: NOREF. Reference data NOT LISTED in test case. -148: [17:55:20] Molecule does not have explicit Hs. Consider calling AddHs() -141: [17:55:20] Rep: 0 Mol:1 -141: [17:55:20] Rep: 0 Mol:0 -141: [17:55:20] Rep: 0 Mol:5 168: 3: res= O=C(O[*:2])[*:1],OC(c1ccccc1)[*:1].c1ccc(C[*:2])cc1 168: 3: NOREF. Reference data NOT LISTED in test case. 168: 4: res= O=C(O[*:1])C(c1ccccc1)[*:2],O[*:2].c1ccc(C[*:1])cc1 @@ -28794,27 +28688,27 @@ 168: 8: NOREF. Reference data NOT LISTED in test case. 168: 9: res= O=C(OC[*:2])C(c1ccccc1)[*:1],O[*:1].c1ccc([*:2])cc1 168: 9: NOREF. Reference data NOT LISTED in test case. -160: file testGithub3226_3.png gave hash 1938488947U not the expected 3119571946U -148: [17:55:20] Molecule does not have explicit Hs. Consider calling AddHs() 168: 10: res= O=C(OC[*:2])C([*:1])[*:3],O[*:1].c1ccc([*:2])cc1.c1ccc([*:3])cc1 168: 10: NOREF. Reference data NOT LISTED in test case. -161: 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 168: 11: res= O=C(OC[*:1])C(O)[*:2],c1ccc([*:1])cc1.c1ccc([*:2])cc1 168: 11: NOREF. Reference data NOT LISTED in test case. 168: 12: res= NULL,O=C(OCc1ccccc1)[*:1].OC(c1ccccc1)[*:1] 168: 12: NOREF. Reference data NOT LISTED in test case. +68: Test +68: +68: BMS-986142_atropBad2.mrv +68: +68: [14:17:42] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +161: Done +161: ----------------- Test 3: test reactant highlighting 168: 13: res= c1ccc(C([*:1])[*:2])cc1,O=C(OCc1ccccc1)[*:1].O[*:2] 168: 13: NOREF. Reference data NOT LISTED in test case. -89: [17:55:20] Explicit valence for atom # 27 P, 6, is greater than permitted 168: 14: res= C([*:1])([*:2])[*:3],O=C(OCc1ccccc1)[*:1].O[*:2].c1ccc([*:3])cc1 168: 14: PASSED. matchedRefRes = 1 -141: [17:55:20] Rep: 0 Mol:4 168: 15: res= OC([*:1])[*:2],O=C(OCc1ccccc1)[*:1].c1ccc([*:2])cc1 168: 15: NOREF. Reference data NOT LISTED in test case. -141: [17:55:20] Rep: 0 Mol:9 168: 16: res= NULL,O=C(OCc1ccccc1)C(c1ccccc1)[*:1].O[*:1] 168: 16: NOREF. Reference data NOT LISTED in test case. -160: file testPNGMetadata_1.png gave hash 3033029091U not the expected 997629701U 168: 17: res= O=C(OCc1ccccc1)C([*:1])[*:2],O[*:1].c1ccc([*:2])cc1 168: 17: NOREF. Reference data NOT LISTED in test case. 168: 18: res= NULL,O=C(OCc1ccccc1)C(O)[*:1].c1ccc([*:1])cc1 @@ -28823,235 +28717,59 @@ 168: --- ALL PASSED --- 168: ----------------------------------- 168: 5 TEST CASES FAILED -131/236 Test #168: testMMPA ............................... Passed 0.16 sec -test 173 - Start 173: testSynthonSpaceSubstructureSearch +130/236 Test #168: testMMPA ............................... Passed 0.46 sec +test 170 + Start 170: testRascalMCES -173: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch -173: Test timeout computed to be: 1500 -148: [17:55:20] Molecule does not have explicit Hs. Consider calling AddHs() -141: [17:55:20] Rep: 0 Mol:6 -141: [17:55:20] Rep: 0 Mol:13 -148: ..[17:55:20] Molecule does not have explicit Hs. Consider calling AddHs() -141: [17:55:20] Rep: 0 Mol:10 -141: [17:55:20] Rep: 0 Mol:8 -159: processing -159: launch :0 -161: file rxn_test2_2_1.png gave hash 457778262U not the expected 1268122583U -141: [17:55:20] Rep: 0 Mol:17 -159: launch :1 -141: [17:55:20] Rep: 0 Mol:12 -159: launch :2 -159: launch :3 -108: .[17:55:20] SMILES Parse Error: syntax error while parsing: mydoghasfleas -108: [17:55:20] SMILES Parse Error: check for mistakes around position 1: -108: [17:55:20] mydoghasfleas -108: [17:55:20] ^ -108: [17:55:20] SMILES Parse Error: Failed parsing SMILES 'mydoghasfleas' for input: 'mydoghasfleas' -141: [17:55:20] Rep: 0 Mol:16 -161: 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 -148: [17:55:20] Molecule does not have explicit Hs. Consider calling AddHs() -148: [17:55:20] Molecule does not have explicit Hs. Consider calling AddHs() -148: [17:55:20] Molecule does not have explicit Hs. Consider calling AddHs() -148: [17:55:20] Molecule does not have explicit Hs. Consider calling AddHs() -148: [17:55:20] Molecule does not have explicit Hs. Consider calling AddHs() -148: [17:55:20] Molecule does not have explicit Hs. Consider calling AddHs() -148: [17:55:20] Molecule does not have explicit Hs. Consider calling AddHs() -148: [17:55:20] Molecule does not have explicit Hs. Consider calling AddHs() -148: [17:55:20] Molecule does not have explicit Hs. Consider calling AddHs() -148: [17:55:20] Molecule does not have explicit Hs. Consider calling AddHs() -160: file testPNGMetadata_2.png gave hash 2637596984U not the expected 1797853056U -141: [17:55:20] Rep: 0 Mol:20 -148: ..[17:55:20] Molecule does not have explicit Hs. Consider calling AddHs() -156: . -156: ---------------------------------------------------------------------- -156: Ran 1 test in 0.063s -156: -156: OK -156: Testing Shape Helpers wrapper -29: Checking against /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -141: [17:55:20] Rep: 0 Mol:24 -161: file rxn_test2_2_2.png gave hash 4285088210U not the expected 82821108U -141: [17:55:20] Rep: 0 Mol:28 -141: [17:55:20] Rep: 0 Mol:21 -161: 2 Cc1c(cc([nH]1)[c:1]2[cH:2][cH:3][cH:4][cH:5][cH:6]2)[C:7](=[O:8])[NH:9][CH2:10][CH2:11]>>CCc1nc(c(n1[c:1]2[cH:2][cH:3][cH:4][cH:5][cH:6]2)C)[C:7](=[O:8])[NH:9][CH2:10][CH2:11] Cc1c(cc([nH]1)c2ccccc2)C(=O)NCCN3CCN(C -161: 2 C3)c4cccc(c4Cl)Cl CCc1nc(c(n1c2ccccc2)C)C(=O)NCCN3CCN(CC3)c4cccc(c4Cl)Cl -161: 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 -148: .[17:55:20] Molecule does not have explicit Hs. Consider calling AddHs() -125: Warning: Atom Count for residue GLU53A does not match expected count -141: [17:55:20] Rep: 0 Mol:25 -148: [17:55:20] Molecule does not have explicit Hs. Consider calling AddHs() -161: file rxn_test2_2_3.png gave hash 660865433U not the expected 3828365604U -161: 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 -141: [17:55:20] Rep: 0 Mol:14 -148: [17:55:20] Molecule does not have explicit Hs. Consider calling AddHs() -141: [17:55:20] Rep: 0 Mol:29 -148: [17:55:20] Molecule does not have explicit Hs. Consider calling AddHs() -132/236 Test #156: pyShapeHelpers ......................... Passed 0.50 sec -161: file rxn_test2_2_4.png gave hash 1904681261U not the expected 1230108677U -test 174 - Start 174: testSynthonSpaceRascalSearch +170: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES/testRascalMCES +170: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES +170: Test timeout computed to be: 1500 +89: [14:17:42] Explicit valence for atom # 3 Al, 6, is greater than permitted +60: Test +60: +60: AtropCanon1.cxsmi +60: +60: Test +60: +60: AtropCanon2.cxsmi +60: +60: Test +60: +60: AtropCanon3.cxsmi +60: +60: Test +60: +60: BMS-986142_3d_chiral.cxsmi +60: +60: Test +60: +60: BMS-986142_3d.cxsmi +60: +60: =============================================================================== +60: All tests passed (2496 assertions in 31 test cases) +60: +162: ...[14:17:42] Font file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/Amadeus.ttf not found. +162: [14:17:42] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +131/236 Test #60: cxsmilesTest ........................... Passed 4.88 sec +test 171 + Start 171: testRascalCluster -174: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceRascalSearch -174: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch -174: Test timeout computed to be: 1500 -161: Done -161: ----------------- Test 3: test reactant highlighting -148: [17:55:20] Molecule does not have explicit Hs. Consider calling AddHs() -148: [17:55:20] Molecule does not have explicit Hs. Consider calling AddHs() -148: [17:55:20] Molecule does not have explicit Hs. Consider calling AddHs() -148: [17:55:20] Molecule does not have explicit Hs. Consider calling AddHs() -148: [17:55:20] Molecule does not have explicit Hs. Consider calling AddHs() -148: [17:55:20] Molecule does not have explicit Hs. Consider calling AddHs() -141: [17:55:20] Rep: 0 Mol:7 -141: [17:55:20] Rep: 0 Mol:11 -141: [17:55:20] Rep: 0 Mol:18 -141: [17:55:20] Rep: 0 Mol:15 -141: [17:55:20] Rep: 0 Mol:19 -141: [17:55:20] Rep: 0 Mol:23 -141: [17:55:20] Rep: 0 Mol:27 -126: Warning: Atom Count for residue ASN39A does not match expected count -154: ..[17:55:20] Molecule does not have explicit Hs. Consider calling AddHs() -160: [17:55:21] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [17:55:21] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. -148: [17:55:21] Molecule does not have explicit Hs. Consider calling AddHs() -141: [17:55:21] Rep: 0 Mol:31 -141: [17:55:21] Rep: 0 Mol:22 -154: .[17:55:21] Molecule does not have explicit Hs. Consider calling AddHs() -160: file testHandDrawn-1.svg gave hash 2072486955U not the expected 2253418236U -148: [17:55:21] Molecule does not have explicit Hs. Consider calling AddHs() -160: [17:55:21] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [17:55:21] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. -154: .[17:55:21] SMARTS Parse Error: syntax error while parsing: [N,O;!HQ] -154: [17:55:21] SMARTS Parse Error: Failed parsing SMARTS '[N,O;!HQ]' for input: '[N,O;!HQ]' +171: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES/testRascalCluster +171: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES +171: Test timeout computed to be: 1500 161: file rxn_test3_1.png gave hash 786828249U not the expected 4189980366U -154: ... -154: ---------------------------------------------------------------------- -154: Ran 9 tests in 0.260s -154: -154: OK -148: [17:55:21] Molecule does not have explicit Hs. Consider calling AddHs() -141: [17:55:21] Rep: 0 Mol:26 161: Done 161: ----------------- Test 4: some examples from SMARTS in testing 161: draw! -148: [17:55:21] Molecule does not have explicit Hs. Consider calling AddHs() -148: [17:55:21] Molecule does not have explicit Hs. Consider calling AddHs() -108: ....... -108: ---------------------------------------------------------------------- -108: Ran 21 tests in 1.050s -108: -108: OK -108: (Five aromatic carbons And (Not any of Five aromatic carbons)) -108: (Five aromatic carbons Or (Not any of Five aromatic carbons)) -108: (Not (Five aromatic carbons And (Not any of Five aromatic carbons))) -108: ******************************************** -108: Testing: PAINS_A 2 -108: ******************************************** -108: Testing: PAINS_B 4 -108: ******************************************** -108: Testing: PAINS_C 8 -108: ******************************************** -108: Testing: PAINS 14 -108: (Not FilterMatcher) -108: Bar -108: Count 1 -108: ******************************************** -108: {'Cl,Br,I'} -108: 1 -108: 2 -108: running -148: [17:55:21] Molecule does not have explicit Hs. Consider calling AddHs() -160: file testHandDrawn-1.png gave hash 70252907U not the expected 3894611804U -141: [17:55:21] Rep: 0 Mol:30 -148: [17:55:21] Molecule does not have explicit Hs. Consider calling AddHs() -148: [17:55:21] Molecule does not have explicit Hs. Consider calling AddHs() -148: [17:55:21] Molecule does not have explicit Hs. Consider calling AddHs() -161: file rxn_test4_1.png gave hash 1704194173U not the expected 2745201873U -148: [17:55:21] Molecule does not have explicit Hs. Consider calling AddHs() -148: [17:55:21] Molecule does not have explicit Hs. Consider calling AddHs() -161: done -148: [17:55:21] Molecule does not have explicit Hs. Consider calling AddHs() -148: [17:55:21] Molecule does not have explicit Hs. Consider calling AddHs() -148: [17:55:21] Molecule does not have explicit Hs. Consider calling AddHs() -148: [17:55:21] Molecule does not have explicit Hs. Consider calling AddHs() -148: [17:55:21] Molecule does not have explicit Hs. Consider calling AddHs() -167: .... -167: ---------------------------------------------------------------------- -167: Ran 4 tests in 0.014s -167: -167: OK -148: [17:55:21] Molecule does not have explicit Hs. Consider calling AddHs() -133/236 Test #108: pyFilterCatalog ........................ Passed 1.39 sec -test 175 - Start 175: testCIPLabeler - -175: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/testCIPLabeler -175: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler -175: Test timeout computed to be: 1500 -148: [17:55:21] Molecule does not have explicit Hs. Consider calling AddHs() -126: Warning: Atom Count for residue GLU53A does not match expected count -148: [17:55:21] Molecule does not have explicit Hs. Consider calling AddHs() -148: [17:55:21] Molecule does not have explicit Hs. Consider calling AddHs() -125: Warning: Atom Count for residue ARG64A does not match expected count -148: [17:55:21] Molecule does not have explicit Hs. Consider calling AddHs() -148: [17:55:21] Molecule does not have explicit Hs. Consider calling AddHs() -29: All 191 tests passed -160: [17:55:21] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [17:55:21] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. -134/236 Test #167: pyMolHash .............................. Passed 0.42 sec -test 176 - Start 176: pyCIPLabelsWrapTest - -176: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/Wrap/pyCIPLabelWrapTest.py" -176: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap -176: Test timeout computed to be: 1500 -162: ...[17:55:21] Font file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/Amadeus.ttf not found. -162: [17:55:21] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. -148: [17:55:21] Molecule does not have explicit Hs. Consider calling AddHs() -148: [17:55:21] Molecule does not have explicit Hs. Consider calling AddHs() -161: file rxn_test4_2.png gave hash 30753303U not the expected 3094925886U -148: [17:55:21] Molecule does not have explicit Hs. Consider calling AddHs() -160: file testHandDrawn-2.svg gave hash 1534109833U not the expected 794717511U -148: [17:55:21] Molecule does not have explicit Hs. Consider calling AddHs() -160: [17:55:21] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [17:55:21] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. -148: [17:55:21] Molecule does not have explicit Hs. Consider calling AddHs() -148: [17:55:21] Molecule does not have explicit Hs. Consider calling AddHs() -161: Done -135/236 Test #161: moldraw2DRxnTest1 ...................... Passed 0.63 sec -test 177 - Start 177: pyCIPLabelsValidation - -177: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/Wrap/pyCIPLabelsValidation.py" -177: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap -177: Test timeout computed to be: 1500 -148: [17:55:21] Molecule does not have explicit Hs. Consider calling AddHs() -148: [17:55:21] Molecule does not have explicit Hs. Consider calling AddHs() -160: file testHandDrawn-2.png gave hash 4273438430U not the expected 1443443188U -160: [17:55:21] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [17:55:21] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. -148: [17:55:21] Molecule does not have explicit Hs. Consider calling AddHs() -136/236 Test #154: pyChemicalFeatures ..................... Passed 0.76 sec -175: Randomness seeded to: 3726750771 -175: [17:55:21] non kekulizable aromatic bond being treated as bond order 1 -175: [17:55:21] non kekulizable aromatic bond being treated as bond order 1 -175: [17:55:21] non kekulizable aromatic bond being treated as bond order 1 -175: [17:55:21] non kekulizable aromatic bond being treated as bond order 1 -175: [17:55:21] non kekulizable aromatic bond being treated as bond order 1 -175: [17:55:21] non kekulizable aromatic bond being treated as bond order 1 -test 178 - Start 178: deprotectTest - -178: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/deprotectTest -178: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect -178: Test timeout computed to be: 1500 -160: file testHandDrawn-3.svg gave hash 2359787964U not the expected 3982694296U -160: [17:55:21] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [17:55:21] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. -148: [17:55:21] Molecule does not have explicit Hs. Consider calling AddHs() -162: ..........[17:55:21] +143: processing +143: launch :0 +143: launch :1 +143: launch :2 +143: launch :3 +160: [14:17:42] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [14:17:42] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +143: [14:17:42] Rep: 0 Mol:2 +162: ..........[14:17:42] 162: 162: **** 162: Pre-condition Violation @@ -29065,7 +28783,7 @@ 162: 2# RDKit::prepMolForDrawing(RDKit::ROMol const*, bool, bool, bool, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/Draw/rdMolDraw2D.so 162: 3# boost::python::objects::caller_py_function_impl, boost::mpl::vector7 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/Draw/rdMolDraw2D.so 162: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -162: 5# 0x00007F69A7CDF62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +162: 5# 0x00007FD763DB862C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 162: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 162: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 162: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so @@ -29076,17 +28794,17 @@ 162: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 162: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 162: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -162: 16# 0x00007F69A61B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -162: 17# 0x00007F69A61B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -162: 18# 0x00007F69A61B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -162: 19# 0x00007F69A61B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -162: 20# 0x00007F69A61B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +162: 16# 0x00007FD7627B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +162: 17# 0x00007FD7627B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +162: 18# 0x00007FD7627B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +162: 19# 0x00007FD7627B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +162: 20# 0x00007FD7627B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 162: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 162: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 162: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 162: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 162: 25# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -162: 26# 0x00007F69A7CDC3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +162: 26# 0x00007FD763DB53C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 162: 27# _PyObject_MakeTpCall in /usr/bin/python3 162: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 162: 29# 0x00000000005CD3C9 in /usr/bin/python3 @@ -29118,90 +28836,428 @@ 162: 55# 0x00000000006B921E in /usr/bin/python3 162: 56# Py_RunMain in /usr/bin/python3 162: 57# Py_BytesMain in /usr/bin/python3 -162: 58# 0x00007F69A8F18CA8 in /lib/x86_64-linux-gnu/libc.so.6 +162: 58# 0x00007FD76542DCA8 in /lib/x86_64-linux-gnu/libc.so.6 162: 59# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 162: 60# _start in /usr/bin/python3 162: ---------- 162: **** 162: -148: [17:55:21] Molecule does not have explicit Hs. Consider calling AddHs() -141: [17:55:21] Rep: 20 Mol:0 -141: [17:55:21] Rep: 20 Mol:4 -141: [17:55:21] Rep: 20 Mol:8 -141: [17:55:21] Rep: 20 Mol:12 -141: [17:55:21] Rep: 20 Mol:16 -141: [17:55:21] Rep: 20 Mol:20 +143: [14:17:42] Rep: 0 Mol:1 +143: [14:17:42] Rep: 0 Mol:5 +143: [14:17:42] Rep: 0 Mol:3 +143: [14:17:42] Rep: 0 Mol:0 +160: file testHandDrawn-1.svg gave hash 2072486955U not the expected 2253418236U +160: [14:17:42] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [14:17:42] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +143: [14:17:42] Rep: 0 Mol:9 +141: [14:17:42] Rep: 60 Mol:1 +141: [14:17:42] Rep: 60 Mol:5 +141: [14:17:42] Rep: 60 Mol:9 +141: [14:17:42] Rep: 60 Mol:13 +141: [14:17:42] Rep: 60 Mol:17 +68: Test +68: +68: JDQ443_3d.mrv +68: +68: Test +68: +68: JDQ443_atrop1.mrv +68: +68: Test +68: +68: JDQ443_atrop2.mrv +68: +68: Test +68: +68: JDQ443_atrop3.mrv +68: +68: Test +68: +68: JDQ443_atropBad1.mrv +68: +68: [14:17:42] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +132/236 Test #108: pyFilterCatalog ........................ Passed 4.05 sec +test 172 + Start 172: pyRascalMCES + +172: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/Wrap/testRascalMCES.py" +172: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES/Wrap +172: Test timeout computed to be: 1500 +143: [14:17:42] Rep: 0 Mol:4 +143: [14:17:42] Rep: 0 Mol:6 +143: [14:17:42] Rep: 0 Mol:10 +143: [14:17:42] Rep: 0 Mol:13 +141: [14:17:42] Rep: 60 Mol:21 +141: [14:17:42] Rep: 60 Mol:25 +141: [14:17:42] Rep: 60 Mol:29 +89: [14:17:42] Explicit valence for atom # 4 Al, 6, is greater than permitted +125: Warning: Atom Count for residue ARG64A does not match expected count +141: [14:17:42] Rep: 60 Mol:3 +141: [14:17:42] Rep: 60 Mol:7 +141: [14:17:42] Rep: 60 Mol:11 +141: [14:17:42] Rep: 60 Mol:15 +141: [14:17:42] Rep: 60 Mol:19 +141: [14:17:42] Rep: 60 Mol:23 +141: [14:17:42] Rep: 60 Mol:27 +141: [14:17:42] Rep: 60 Mol:31 +143: [14:17:42] Rep: 0 Mol:7 +143: [14:17:42] Rep: 0 Mol:17 +167: .... +167: ---------------------------------------------------------------------- +167: Ran 4 tests in 0.079s +167: +167: OK +143: [14:17:42] Rep: 0 Mol:11 +143: [14:17:42] Rep: 0 Mol:15 +143: [14:17:42] Rep: 0 Mol:8 +89: [14:17:42] Explicit valence for atom # 10 Si, 6, is greater than permitted +143: [14:17:42] Rep: 0 Mol:19 +143: [14:17:42] Rep: 0 Mol:14 +143: [14:17:42] Rep: 0 Mol:12 +143: [14:17:42] Rep: 0 Mol:16 +141: [14:17:42] Rep: 40 Mol:2 +141: [14:17:42] Rep: 40 Mol:6 +143: [14:17:42] Rep: 0 Mol:23 +143: [14:17:42] Rep: 0 Mol:27 +143: [14:17:42] Rep: 0 Mol:18 +141: [14:17:42] Rep: 60 Mol:0 +141: [14:17:42] Rep: 60 Mol:4 +141: [14:17:42] Rep: 60 Mol:8 +141: [14:17:42] Rep: 60 Mol:12 +141: [14:17:42] Rep: 40 Mol:10 +141: [14:17:42] Rep: 40 Mol:14 +141: [14:17:42] Rep: 40 Mol:18 +141: [14:17:42] Rep: 40 Mol:22 +141: [14:17:42] Rep: 40 Mol:26 +141: [14:17:42] Rep: 60 Mol:16 +141: [14:17:42] Rep: 60 Mol:20 +141: [14:17:42] Rep: 60 Mol:24 +141: [14:17:42] Rep: 60 Mol:28 +126: Warning: Atom Count for residue GLU53A does not match expected count +143: [14:17:42] Rep: 0 Mol:21 +143: [14:17:42] Rep: 0 Mol:31 +141: [14:17:42] Rep: 40 Mol:30 +143: [14:17:42] Rep: 0 Mol:20 +143: [14:17:42] Rep: 0 Mol:25 +143: [14:17:42] Rep: 0 Mol:22 +143: [14:17:42] Rep: 0 Mol:26 +143: [14:17:42] Rep: 0 Mol:24 +143: [14:17:42] Rep: 0 Mol:29 +143: [14:17:42] Rep: 0 Mol:28 +143: [14:17:42] Rep: 0 Mol:30 +161: file rxn_test4_1.png gave hash 1704194173U not the expected 2745201873U +160: file testHandDrawn-1.png gave hash 70252907U not the expected 3894611804U +69: ---------------------------------- +69: ---------------------------------- +69: [14:17:42] +69: +69: **** +69: Pre-condition Violation +69: rlabel out of range for MDL files +69: Violation occurred on line 863 in file ./Code/GraphMol/Atom.cpp +69: Failed Expression: rlabel >= 0 && rlabel < 100 +69: ---------- +69: Stacktrace: +69: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +69: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +69: 2# RDKit::setAtomRLabel(RDKit::Atom*, int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +69: 3# 0x000055AD5A89EFFF in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 4# 0x000055AD5A8F83EA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 5# 0x000055AD5A878923 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 6# 0x00007FECAE833CA8 in /lib/x86_64-linux-gnu/libc.so.6 +69: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +69: 8# 0x000055AD5A878AD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: ---------- +69: **** +69: +69: [14:17:42] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +133/236 Test #167: pyMolHash .............................. Passed 1.01 sec +test 173 + Start 173: testSynthonSpaceSubstructureSearch + +173: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch +173: Test timeout computed to be: 1500 +126: Warning: Atom Count for residue ARG64A does not match expected count +141: [14:17:42] Rep: 80 Mol:1 +141: [14:17:42] Rep: 80 Mol:5 +141: [14:17:42] Rep: 80 Mol:9 +141: [14:17:42] Rep: 80 Mol:13 +161: done +141: [14:17:42] Rep: 80 Mol:17 +141: [14:17:42] Rep: 80 Mol:21 +141: [14:17:42] Rep: 80 Mol:25 +141: [14:17:42] Rep: 80 Mol:29 +148: [14:17:42] Molecule does not have explicit Hs. Consider calling AddHs() +68: Test +68: +68: RP-6306_atrop1.mrv +68: +68: Test +68: +68: RP-6306_atrop2.mrv +68: +68: Test +68: +68: RP-6306_atrop3.mrv +68: +68: Test +68: +68: RP-6306_atrop4.mrv +68: +68: Test +68: +68: RP-6306_atrop5.mrv +68: +68: [14:17:42] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +68: [14:17:42] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +156: . +156: ---------------------------------------------------------------------- +156: Ran 1 test in 1.043s +156: +156: OK +156: Testing Shape Helpers wrapper +68: Test +68: +68: RP-6306_atropBad1.mrv +68: +68: [14:17:42] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +160: [14:17:42] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [14:17:42] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +68: Test +68: +68: RP-6306_atropBad2.mrv +68: +68: [14:17:42] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +68: [14:17:42] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +68: [14:17:42] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +141: [14:17:42] Rep: 80 Mol:3 +141: [14:17:42] Rep: 80 Mol:7 +141: [14:17:42] Rep: 80 Mol:11 +141: [14:17:42] Rep: 80 Mol:15 +141: [14:17:42] Rep: 80 Mol:19 +141: [14:17:42] Rep: 80 Mol:23 +141: [14:17:42] Rep: 80 Mol:27 +141: [14:17:42] Rep: 80 Mol:31 +160: file testHandDrawn-2.svg gave hash 1534109833U not the expected 794717511U +160: [14:17:42] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [14:17:42] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +130: [14:17:42] done +130: [14:17:42] ------------------------------------- +130: [14:17:42] Test GitHub Issue #6958 +130: [14:17:42] DEPRECATION WARNING: please use AtomPairGenerator +134/236 Test #130: testFingerprintGenerators .............. Passed 3.54 sec +test 174 + Start 174: testSynthonSpaceRascalSearch + +174: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceRascalSearch +174: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch +174: Test timeout computed to be: 1500 +161: file rxn_test4_2.png gave hash 30753303U not the expected 3094925886U +161: Done +135/236 Test #161: moldraw2DRxnTest1 ...................... Passed 1.90 sec +test 175 + Start 175: testCIPLabeler + +175: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/testCIPLabeler +175: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler +175: Test timeout computed to be: 1500 +160: file testHandDrawn-2.png gave hash 4273438430U not the expected 1443443188U +160: [14:17:43] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [14:17:43] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +160: file testHandDrawn-3.svg gave hash 2359787964U not the expected 3982694296U +160: [14:17:43] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [14:17:43] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +136/236 Test #156: pyShapeHelpers ......................... Passed 2.16 sec +test 176 + Start 176: pyCIPLabelsWrapTest + +176: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/Wrap/pyCIPLabelWrapTest.py" +176: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap +176: Test timeout computed to be: 1500 160: file testHandDrawn-3.png gave hash 258221924U not the expected 865629432U -160: [17:55:21] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [17:55:21] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. -141: [17:55:21] Rep: 20 Mol:24 +141: [14:17:43] Rep: 60 Mol:2 +141: [14:17:43] Rep: 60 Mol:6 +141: [14:17:43] Rep: 60 Mol:10 +141: [14:17:43] Rep: 60 Mol:14 +141: [14:17:43] Rep: 60 Mol:18 +141: [14:17:43] Rep: 60 Mol:22 +141: [14:17:43] Rep: 60 Mol:26 +160: [14:17:43] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [14:17:43] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. 160: file testHandDrawn-4.svg gave hash 1880974760U not the expected 2146113517U -141: [17:55:21] Rep: 20 Mol:28 -160: [17:55:21] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [17:55:21] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +141: [14:17:43] Rep: 60 Mol:30 +160: [14:17:43] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [14:17:43] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +68: Test +68: +68: RP-6306_3d.mrv +68: +68: Test +68: +68: Sotorasib_atrop1.mrv +68: +68: Test +68: +68: Sotorasib_atrop2.mrv +68: +68: Test +68: +68: Sotorasib_atrop3.mrv +68: +68: Test +68: +68: Sotorasib_atrop4.mrv +68: +68: Test +68: +68: Sotorasib_atrop5.mrv +68: +68: [14:17:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +68: [14:17:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +175: Randomness seeded to: 2495843903 +175: [14:17:43] non kekulizable aromatic bond being treated as bond order 1 +175: [14:17:43] non kekulizable aromatic bond being treated as bond order 1 +175: [14:17:43] non kekulizable aromatic bond being treated as bond order 1 +175: [14:17:43] non kekulizable aromatic bond being treated as bond order 1 +175: [14:17:43] non kekulizable aromatic bond being treated as bond order 1 +175: [14:17:43] non kekulizable aromatic bond being treated as bond order 1 160: file testHandDrawn-4.png gave hash 2602629668U not the expected 3919767093U -126: Warning: Atom Count for residue ARG64A does not match expected count -148: [17:55:21] Molecule does not have explicit Hs. Consider calling AddHs() -141: [17:55:21] Rep: 20 Mol:3 -148: [17:55:21] Molecule does not have explicit Hs. Consider calling AddHs() -141: [17:55:21] Rep: 20 Mol:7 -141: [17:55:21] Rep: 20 Mol:11 -141: [17:55:21] Rep: 20 Mol:15 -141: [17:55:21] Rep: 20 Mol:19 -141: [17:55:21] Rep: 20 Mol:23 -141: [17:55:21] Rep: 20 Mol:27 -141: [17:55:21] Rep: 20 Mol:31 -178: Randomness seeded to: 3927252705 -178: =============================================================================== -178: All tests passed (111 assertions in 3 test cases) -178: -137/236 Test #178: deprotectTest .......................... Passed 0.09 sec +68: Test +68: +68: Sotorasib_atropBad1.mrv +68: +68: [14:17:43] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +141: [14:17:43] Rep: 80 Mol:0 +141: [14:17:43] Rep: 80 Mol:4 +141: [14:17:43] Rep: 80 Mol:8 +141: [14:17:43] Rep: 80 Mol:12 +141: [14:17:43] Rep: 80 Mol:16 +141: [14:17:43] Rep: 80 Mol:20 +141: [14:17:43] Rep: 80 Mol:24 +141: [14:17:43] Rep: 80 Mol:28 +68: Test +68: +68: Sotorasib_atropBad2.mrv +68: +68: [14:17:43] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +126: Warning: Atom Count for residue LYS80A does not match expected count +162: ...................... +162: ---------------------------------------------------------------------- +162: Ran 35 tests in 1.017s +162: +162: OK +162: json lasso +40: [14:17:43] done: 500000 +40: [14:17:43] Done +89: [14:17:43] Explicit valence for atom # 2 O, 4, is greater than permitted +89: [14:17:43] Explicit valence for atom # 3 Al, 6, is greater than permitted +89: [14:17:43] Explicit valence for atom # 3 Be, 4, is greater than permitted +125: Warning: Atom Count for residue LYS80A does not match expected count +175: [14:17:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +175: [14:17:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +89: [14:17:43] Explicit valence for atom # 27 P, 6, is greater than permitted +68: Test +68: +68: Sotorasib_3d.mrv +68: +68: Test +68: +68: ZM374979_atrop1.mrv +68: +68: Test +68: +68: ZM374979_atrop2.mrv +68: +68: Test +68: +68: ZM374979_atrop3.mrv +68: +68: Test +68: +68: ZM374979_atropBad1.mrv +68: +68: [14:17:43] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +175: =============================================================================== +175: All tests passed (6577 assertions in 19 test cases) +175: +137/236 Test #175: testCIPLabeler ......................... Passed 0.42 sec +test 177 + Start 177: pyCIPLabelsValidation + +177: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/Wrap/pyCIPLabelsValidation.py" +177: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap +177: Test timeout computed to be: 1500 +40: [14:17:43] Testing hanoi with a functor. +40: [14:17:43] Done +40: [14:17:43] Testing basic partition refinement. +40: [14:17:43] Done +40: [14:17:43] Testing partition refinement with neighbors. +40: [14:17:43] Done +40: [14:17:43] testing canonicalization via tie breaking. +40: [14:17:43] Done +40: [14:17:43] testing canonicalization using the wrapper. +89: =============================================================================== +89: All tests passed (21562 assertions in 3 test cases) +89: +138/236 Test #89: multithreadedSupplierCatchTest ......... Passed 5.43 sec +test 178 + Start 178: deprotectTest + +178: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/deprotectTest +178: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect +178: Test timeout computed to be: 1500 +139/236 Test #162: pyMolDraw2D ............................ Passed 2.45 sec test 179 Start 179: pyDeprotect 179: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Deprotect/Wrap/rough_test.py" 179: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/Wrap 179: Test timeout computed to be: 1500 -69: [17:55:21] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas -148: [17:55:21] Molecule does not have explicit Hs. Consider calling AddHs() -69: [17:55:21] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' -29: -29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.sdf... -148: [17:55:21] Molecule does not have explicit Hs. Consider calling AddHs() -130: [17:55:21] done -130: [17:55:21] ------------------------------------- -130: [17:55:21] Test GitHub Issue #6958 -130: [17:55:21] DEPRECATION WARNING: please use AtomPairGenerator -138/236 Test #130: testFingerprintGenerators .............. Passed 1.31 sec +68: Test +68: +68: mrtx1719_3d.mrv +68: +68: Test +68: +68: mrtx1719_atrop1.mrv +68: +68: Test +68: +68: mrtx1719_atrop2.mrv +68: +68: Test +68: +68: mrtx1719_atrop3.mrv +68: +68: Test +68: +68: mrtx1719_atropBad1.mrv +68: +68: [14:17:43] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +40: [14:17:43] Done +40: [14:17:43] testing some specific ordering problems +40: [14:17:43] Finished +40: [14:17:43] testing chiral invariants. +40: [14:17:43] Finished +40: [14:17:43] testing unique ranks in w.r.t. renumbering. +117: =>start test GETAWAY custom +117: [14:17:43] test on : 365 molecules done +140/236 Test #117: testRDFcustom .......................... Passed 4.97 sec +141: [14:17:43] Rep: 80 Mol:2 test 180 Start 180: testReducedGraphs 180: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/testReducedGraphs 180: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs 180: Test timeout computed to be: 1500 -141: [17:55:21] Rep: 20 Mol:1 -141: [17:55:21] Rep: 20 Mol:5 -141: [17:55:21] Rep: 20 Mol:9 -141: [17:55:21] Rep: 20 Mol:13 -141: [17:55:21] Rep: 20 Mol:17 -141: [17:55:21] Rep: 20 Mol:21 -141: [17:55:21] Rep: 20 Mol:25 -141: [17:55:21] Rep: 20 Mol:29 -162: ...................... -162: ---------------------------------------------------------------------- -162: Ran 35 tests in 0.252s -162: -162: OK -162: json lasso -143: [17:55:21] Rep: 100 Mol:3 -143: [17:55:21] Rep: 100 Mol:7 -143: [17:55:21] Rep: 100 Mol:11 -143: [17:55:21] Rep: 100 Mol:15 -143: [17:55:21] Rep: 100 Mol:19 -143: [17:55:21] Rep: 100 Mol:23 -143: [17:55:21] Rep: 100 Mol:27 -143: [17:55:21] Rep: 100 Mol:31 -148: [17:55:21] Molecule does not have explicit Hs. Consider calling AddHs() +141: [14:17:43] Rep: 80 Mol:6 +141: [14:17:43] Rep: 80 Mol:10 +141: [14:17:43] Rep: 80 Mol:14 +141: [14:17:43] Rep: 80 Mol:18 +141: [14:17:43] Rep: 80 Mol:22 +141: [14:17:43] Rep: 80 Mol:26 +141: [14:17:43] Rep: 80 Mol:30 180: Size: 315 [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ] 180: 180: Size: 315 [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0.3, 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, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ] @@ -29216,115 +29272,231 @@ 180: 180: 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, 0.3, 1, 0.3, 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, 0.3, 1, 0.3, 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, 0.3, 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, ] 180: -139/236 Test #162: pyMolDraw2D ............................ Passed 0.87 sec +180: 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, 0.3, 1, 0.3, 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, 0.3, 1, 0.3, 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, 0.3, 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, ] +180: +180: 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, ] +180: +141/236 Test #180: testReducedGraphs ...................... Passed 0.15 sec test 181 Start 181: pyReducedGraphs 181: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ReducedGraphs/Wrap/testReducedGraphs.py" 181: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap 181: Test timeout computed to be: 1500 -180: 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, 0.3, 1, 0.3, 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, 0.3, 1, 0.3, 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, 0.3, 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, ] -180: -180: 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, ] -180: -141: [17:55:21] Rep: 40 Mol:3 -141: [17:55:21] Rep: 40 Mol:7 -141: [17:55:21] Rep: 40 Mol:11 -141: [17:55:21] Rep: 40 Mol:15 -141: [17:55:21] Rep: 40 Mol:19 -141: [17:55:21] Rep: 40 Mol:23 -89: [17:55:21] Explicit valence for atom # 9 N, 5, is greater than permitted -140/236 Test #180: testReducedGraphs ...................... Passed 0.09 sec +148: [14:17:43] Molecule does not have explicit Hs. Consider calling AddHs() +40: [14:17:43] Finished +40: [14:17:43] testing mol fragments. +40: [14:17:43] Finished +40: [14:17:43] testing protein round-tripping. +141: [14:17:43] done +141: [14:17:43] ------------------------------------- +141: [14:17:43] Test MMFF multithreading2 +178: Randomness seeded to: 2333115381 +178: =============================================================================== +178: All tests passed (111 assertions in 3 test cases) +178: +142/236 Test #178: deprotectTest .......................... Passed 0.40 sec test 182 Start 182: trajectoryTest 182: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory/trajectoryTest 182: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory 182: Test timeout computed to be: 1500 -148: [17:55:21] Molecule does not have explicit Hs. Consider calling AddHs() -141: [17:55:21] Rep: 40 Mol:27 -141: [17:55:21] Rep: 40 Mol:31 -69: [17:55:21] Empty atom list: 'M ALS 1 0 F' on line 8. -69: de_DE.UTF-8 -69: [17:55:21] ------------------------------------- -69: [17:55:21] Test multithreading Locale Switching -125: Warning: Atom Count for residue LYS80A does not match expected count -117: =>start test morse custom -117: [17:55:21] test on : 365 molecules done -141: [17:55:21] Rep: 20 Mol:2 -141: [17:55:21] Rep: 20 Mol:6 -141: [17:55:21] Rep: 20 Mol:10 -141: [17:55:21] Rep: 20 Mol:14 -141: [17:55:21] Rep: 20 Mol:18 -141: [17:55:21] Rep: 20 Mol:22 -141: [17:55:21] Rep: 20 Mol:26 -141: [17:55:21] Rep: 20 Mol:30 -141: [17:55:21] Rep: 40 Mol:0 -141: [17:55:21] Rep: 40 Mol:4 -175: [17:55:21] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -141: [17:55:21] Rep: 40 Mol:8 -175: [17:55:21] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -126: Warning: Atom Count for residue LYS80A does not match expected count -141: [17:55:21] Rep: 40 Mol:12 -141: [17:55:21] Rep: 40 Mol:16 -141: [17:55:21] Rep: 40 Mol:20 -141: [17:55:21] Rep: 40 Mol:24 -141: [17:55:21] Rep: 40 Mol:28 -69: [17:55:21] Test multithreading (Done) -69: [17:55:21] ------------------------------------- +143: [14:17:44] Rep: 100 Mol:3 +143: [14:17:44] Rep: 100 Mol:7 +143: [14:17:44] Rep: 100 Mol:11 +143: [14:17:44] Rep: 100 Mol:15 +143: [14:17:44] Rep: 100 Mol:19 +143: [14:17:44] Rep: 100 Mol:23 +143: [14:17:44] Rep: 100 Mol:27 +143: [14:17:44] Rep: 100 Mol:31 +68: Test +68: +68: AlexRxn.mrv +68: +68: Test +68: +68: BadReactionSign.mrv +68: +68: Test +68: +68: bondArray_node.mrv +68: +68: Test +68: +68: marvin03.mrv +68: +68: Test +68: +68: marvin04.mrv +68: +68: Test +68: +68: marvin08.mrv +68: +68: Test +68: +68: marvin09.mrv +68: +68: Test +68: +68: marvin11.mrv +68: +68: Test +68: +68: marvin05.mrv +68: +68: Test +68: +68: EmptyRxn.mrv +68: +68: [14:17:44] initialization failed +69: [14:17:44] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas +69: [14:17:44] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' +143: [14:17:44] Rep: 100 Mol:1 +143: [14:17:44] Rep: 100 Mol:5 +143: [14:17:44] Rep: 100 Mol:9 +143: [14:17:44] Rep: 100 Mol:13 +143: [14:17:44] Rep: 100 Mol:17 +143: [14:17:44] Rep: 100 Mol:21 +143: [14:17:44] Rep: 100 Mol:25 +143: [14:17:44] Rep: 100 Mol:29 176: .... 176: ---------------------------------------------------------------------- -176: Ran 4 tests in 0.057s +176: Ran 4 tests in 0.078s 176: 176: OK -69: *************************************** -69: *************************************** -172: ..........[17:55:21] Too many matching bond pairs (1032) so can't continue. -89: [17:55:21] Explicit valence for atom # 3 Al, 6, is greater than permitted -69: [17:55:21] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: [17:55:21] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -148: [17:55:21] Molecule does not have explicit Hs. Consider calling AddHs() -143: [17:55:21] Rep: 100 Mol:1 -69: [17:55:21] bond with order 0 found on line 7. This is not part of the MDL specification. -143: [17:55:21] Rep: 100 Mol:5 -143: [17:55:21] Rep: 100 Mol:9 -143: [17:55:21] Rep: 100 Mol:13 -143: [17:55:21] Rep: 100 Mol:17 -143: [17:55:21] Rep: 100 Mol:21 -143: [17:55:21] Rep: 100 Mol:25 -175: =============================================================================== -175: All tests passed (6577 assertions in 19 test cases) -175: -143: [17:55:21] Rep: 100 Mol:29 -141/236 Test #175: testCIPLabeler ......................... Passed 0.55 sec +68: Test +68: +68: RxnNoCoords.mrv +68: +68: Test +68: +68: mrvValenceZero.mrv +68: +68: Test +68: +68: condition_coordinates_mpoint.mrv +68: +68: Test +68: +68: marvin01.mrv +68: +68: Test +68: +68: aspirineSynthesisWithAttributes.mrv +68: +68: Test +68: +68: marvin01.mrv +68: +68: Test +68: +68: NewChiralTest +68: +68: Test +68: +68: NewChiralTest +68: +68: Test +68: +68: NewChiralTestNoChiral +68: +68: Test +68: +68: NewChiralTestNoChiral +68: +68: Test +68: +68: NewChiralTest2 +68: +68: Test +68: +68: NewChiralTest2 +68: +68: Test +68: +68: NewChiralTest2AllChiral +68: +68: Test +68: +68: NewChiralTest2AllChiral +68: +68: Test +68: +68: Vendor839 +68: +68: Test +68: +68: DoubleBondChain +68: +68: Test +68: +68: Na_Mg_Al_OH +68: +68: Test +68: +68: Pb +68: +68: Test +68: +68: O_Mg_Si +68: +68: Test +68: +68: SquiggleBond +68: +68: Test +68: +68: BigMacrocycle +68: +68: Test +68: +68: Smiles1 +68: +143/236 Test #68: testMrvToMol ........................... Passed 6.76 sec test 183 Start 183: substructLibraryTest 183: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/substructLibraryTest 183: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary 183: Test timeout computed to be: 1500 -148: [17:55:21] Molecule does not have explicit Hs. Consider calling AddHs() -89: [17:55:21] Explicit valence for atom # 4 Al, 6, is greater than permitted -69: [17:55:21] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) -69: [17:55:21] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) -69: [17:55:21] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -181: ..... -181: ---------------------------------------------------------------------- -181: Ran 5 tests in 0.028s -181: -181: OK -89: [17:55:21] Explicit valence for atom # 10 Si, 6, is greater than permitted -69: generating smiles -141: [17:55:21] Rep: 40 Mol:1 -141: [17:55:21] Rep: 40 Mol:5 -141: [17:55:21] Rep: 40 Mol:9 -69: 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 -69: converting back -183: [17:55:21] ------------------------------------- -183: [17:55:21] Test1 +144/236 Test #182: trajectoryTest ......................... Passed 0.55 sec +test 184 + Start 184: substructLibraryCatchTest + +184: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/substructLibraryCatchTest +184: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary +184: Test timeout computed to be: 1500 +145/236 Test #176: pyCIPLabelsWrapTest .................... Passed 1.48 sec +test 185 + Start 185: pySubstructLibrary + +185: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/SubstructLibrary/Wrap/rough_test.py" +185: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap +185: Test timeout computed to be: 1500 +69: [14:17:44] Empty atom list: 'M ALS 1 0 F' on line 8. +183: [14:17:44] ------------------------------------- +183: [14:17:44] Test1 +141: [14:17:44] done +141: [14:17:44] ------------------------------------- +141: [14:17:44] Test MMFF multithreading3 +172: ..........[14:17:44] Too many matching bond pairs (1032) so can't continue. +148: [14:17:44] Molecule does not have explicit Hs. Consider calling AddHs() +69: de_DE.UTF-8 +69: [14:17:45] ------------------------------------- +69: [14:17:45] Test multithreading Locale Switching +143: [14:17:45] Rep: 100 Mol:0 +143: [14:17:45] Rep: 100 Mol:4 +143: [14:17:45] Rep: 100 Mol:8 +143: [14:17:45] Rep: 100 Mol:12 +143: [14:17:45] Rep: 100 Mol:16 +143: [14:17:45] Rep: 100 Mol:20 +143: [14:17:45] Rep: 100 Mol:24 +143: [14:17:45] Rep: 100 Mol:28 179: ..... 179: ---------------------------------------------------------------------- -179: Ran 5 tests in 0.068s +179: Ran 5 tests in 0.751s 179: 179: OK 179: Testing tert-butyldimethylsilyl @@ -29377,362 +29549,182 @@ 179: Testing acetamide 179: Testing carbobenzyloxy 179: Testing Acetal/Ketal -141: [17:55:21] Rep: 40 Mol:13 -141: [17:55:21] Rep: 40 Mol:17 -141: [17:55:21] Rep: 40 Mol:21 -141: [17:55:21] Rep: 40 Mol:25 -69: check isomorphism -143: [17:55:21] Rep: 100 Mol:0 -143: [17:55:21] Rep: 100 Mol:4 -143: [17:55:21] Rep: 100 Mol:8 -143: [17:55:21] Rep: 100 Mol:12 -143: [17:55:21] Rep: 100 Mol:16 -141: [17:55:21] Rep: 40 Mol:29 -143: [17:55:21] Rep: 100 Mol:20 -143: [17:55:21] Rep: 100 Mol:24 -143: [17:55:21] Rep: 100 Mol:28 -141: [17:55:21] Rep: 60 Mol:3 -141: [17:55:21] Rep: 60 Mol:7 -141: [17:55:21] Rep: 60 Mol:11 -141: [17:55:21] Rep: 60 Mol:15 -141: [17:55:21] Rep: 60 Mol:19 -148: [17:55:21] Molecule does not have explicit Hs. Consider calling AddHs() -142/236 Test #176: pyCIPLabelsWrapTest .................... Passed 0.62 sec -test 184 - Start 184: substructLibraryCatchTest - -184: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/substructLibraryCatchTest -184: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary -184: Test timeout computed to be: 1500 -141: [17:55:21] Rep: 60 Mol:23 -141: [17:55:21] Rep: 60 Mol:27 -141: [17:55:21] Rep: 60 Mol:31 -147: [17:55:21] UFFTYPER: Warning: hybridization set to SP3 for atom 6 -143/236 Test #181: pyReducedGraphs ........................ Passed 0.35 sec -test 185 - Start 185: pySubstructLibrary - -185: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/SubstructLibrary/Wrap/rough_test.py" -185: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap -185: Test timeout computed to be: 1500 -144/236 Test #179: pyDeprotect ............................ Passed 0.51 sec +69: [14:17:45] Test multithreading (Done) +69: [14:17:45] ------------------------------------- +69: *************************************** +69: *************************************** +69: [14:17:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [14:17:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [14:17:45] bond with order 0 found on line 7. This is not part of the MDL specification. +146/236 Test #179: pyDeprotect ............................ Passed 1.89 sec test 186 Start 186: testRGroupDecomp 186: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/testRGroupDecomp 186: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition 186: Test timeout computed to be: 1500 -148: [17:55:21] Molecule does not have explicit Hs. Consider calling AddHs() -147: [17:55:21] UFFTYPER: Warning: hybridization set to SP3 for atom 6 -148: [17:55:21] Molecule does not have explicit Hs. Consider calling AddHs() -147: [17:55:21] UFFTYPER: Warning: hybridization set to SP3 for atom 6 -148: [17:55:21] Molecule does not have explicit Hs. Consider calling AddHs() -145/236 Test #182: trajectoryTest ......................... Passed 0.48 sec +69: [14:17:45] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) +69: [14:17:45] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) +69: [14:17:45] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +69: generating smiles +143: [14:17:45] Rep: 100 Mol:2 +143: [14:17:45] Rep: 100 Mol:6 +143: [14:17:45] Rep: 100 Mol:10 +143: [14:17:45] Rep: 100 Mol:14 +69: 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 +69: converting back +69: check isomorphism +143: [14:17:45] Rep: 100 Mol:18 +143: [14:17:45] Rep: 100 Mol:22 +143: [14:17:45] Rep: 100 Mol:26 +143: [14:17:45] Rep: 100 Mol:30 +160: file testHandDrawn-5a.svg gave hash 3327818543U not the expected 1567781555U +160: [14:17:45] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [14:17:45] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +181: ..... +181: ---------------------------------------------------------------------- +181: Ran 5 tests in 0.141s +181: +181: OK +160: file testHandDrawn-5b.svg gave hash 2125846125U not the expected 66354106U +160: [14:17:45] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [14:17:45] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +141: [14:17:45] done +141: [14:17:45] ------------------------------------- +141: [14:17:45] Testing github 162: Incorrect SMILES after MMFF parameterization . +141: [14:17:45] done +141: [14:17:45] ------------------------------------- +141: [14:17:45] Testing github 224: crash during MMFF parameterization . +141: [14:17:45] done +141: [14:17:45] ------------------------------------- +141: [14:17:45] Testing github6728: crash due to missing stretch-bend params. +160: file testHandDrawn-5.png gave hash 2441005674U not the expected 828378555U +147/236 Test #141: testMMFFForceFieldHelpers .............. Passed 5.95 sec test 187 Start 187: testRGroupDecompInternals 187: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/testRGroupDecompInternals 187: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition 187: Test timeout computed to be: 1500 -141: [17:55:21] Rep: 60 Mol:0 -141: [17:55:21] Rep: 60 Mol:4 -141: [17:55:21] Rep: 60 Mol:8 -141: [17:55:21] Rep: 60 Mol:12 -141: [17:55:21] Rep: 60 Mol:16 -148: [17:55:21] Molecule does not have explicit Hs. Consider calling AddHs() -141: [17:55:21] Rep: 40 Mol:2 -141: [17:55:21] Rep: 40 Mol:6 -141: [17:55:21] Rep: 40 Mol:10 -141: [17:55:21] Rep: 40 Mol:14 -141: [17:55:21] Rep: 40 Mol:18 -141: [17:55:21] Rep: 60 Mol:20 -141: [17:55:21] Rep: 40 Mol:22 -141: [17:55:21] Rep: 60 Mol:24 -141: [17:55:21] Rep: 40 Mol:26 -141: [17:55:21] Rep: 60 Mol:28 -141: [17:55:21] Rep: 40 Mol:30 -117: =>start test AUTOCORR3D custom -117: [17:55:21] test on : 365 molecules done -148: [17:55:21] Molecule does not have explicit Hs. Consider calling AddHs() -143: [17:55:21] Rep: 100 Mol:2 -143: [17:55:21] Rep: 100 Mol:6 -143: [17:55:21] Rep: 100 Mol:10 -147: [17:55:21] UFFTYPER: Warning: hybridization set to SP3 for atom 11 -143: [17:55:21] Rep: 100 Mol:14 -143: [17:55:21] Rep: 100 Mol:18 -143: [17:55:21] Rep: 100 Mol:22 -143: [17:55:21] Rep: 100 Mol:26 -147: [17:55:21] UFFTYPER: Warning: hybridization set to SP3 for atom 11 -187: [17:55:21] WARNING: not removing hydrogen atom with dummy atom neighbors -143: [17:55:21] Rep: 100 Mol:30 -187: [17:55:21] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [17:55:21] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [17:55:21] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [17:55:21] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [17:55:21] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [17:55:21] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [17:55:21] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [17:55:21] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [17:55:21] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [17:55:21] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [17:55:21] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [17:55:21] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [17:55:21] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [17:55:21] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [17:55:21] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [17:55:21] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [17:55:21] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [17:55:21] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [17:55:21] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [17:55:21] WARNING: not removing hydrogen atom with dummy atom neighbors -146/236 Test #187: testRGroupDecompInternals .............. Passed 0.09 sec +160: file testBrackets-5a.svg gave hash 279553678U not the expected 1447240271U +126: Warning: Atom Count for residue GLU150A does not match expected count +187: [14:17:45] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [14:17:45] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [14:17:45] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [14:17:45] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [14:17:45] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [14:17:45] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [14:17:45] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [14:17:45] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [14:17:45] WARNING: not removing hydrogen atom with dummy atom neighbors +160: file testPositionVariation-1b.svg gave hash 3055422087U not the expected 3269244452U +126: Warning: Atom Count for residue ASN157A does not match expected count +187: [14:17:45] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [14:17:45] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [14:17:45] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [14:17:45] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [14:17:45] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [14:17:45] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [14:17:45] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [14:17:45] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [14:17:45] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [14:17:45] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [14:17:45] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [14:17:45] WARNING: not removing hydrogen atom with dummy atom neighbors +148/236 Test #187: testRGroupDecompInternals .............. Passed 0.09 sec test 188 Start 188: rgroupCatchTests 188: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/rgroupCatchTests 188: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition 188: Test timeout computed to be: 1500 -148: [17:55:21] Molecule does not have explicit Hs. Consider calling AddHs() -147: [17:55:21] UFFTYPER: Warning: hybridization set to SP3 for atom 11 -89: [17:55:22] Explicit valence for atom # 2 O, 4, is greater than permitted -148: [17:55:22] Molecule does not have explicit Hs. Consider calling AddHs() -89: [17:55:22] Explicit valence for atom # 3 Al, 6, is greater than permitted -89: [17:55:22] Explicit valence for atom # 3 Be, 4, is greater than permitted -89: [17:55:22] Explicit valence for atom # 27 P, 6, is greater than permitted -141: [17:55:22] Rep: 80 Mol:3 -141: [17:55:22] Rep: 80 Mol:7 -141: [17:55:22] Rep: 80 Mol:11 -141: [17:55:22] Rep: 80 Mol:15 -141: [17:55:22] Rep: 80 Mol:19 -141: [17:55:22] Rep: 80 Mol:23 -141: [17:55:22] Rep: 80 Mol:27 -148: [17:55:22] Molecule does not have explicit Hs. Consider calling AddHs() -141: [17:55:22] Rep: 80 Mol:31 -98: . -98: ---------------------------------------------------------------------- -98: Ran 11 tests in 2.143s -98: -98: OK -98: True -98: == CartesianProductStrategy CartesianProductStrategy -98: 197 out of 300 -98: 0 6 out of 10 -98: 1 3 out of 5 -98: 2 4 out of 6 -98: 198 out of 300 -98: 0 10 out of 10 -98: 1 5 out of 5 -98: 2 6 out of 6 -98: Skipped 10000000 in 0.06832170486450195 seconds -98: Skipped 10000000 in 0.8213801383972168 seconds -98: Skipped 10000000 in 0.9523680210113525 seconds -141: [17:55:22] Rep: 60 Mol:1 -141: [17:55:22] Rep: 60 Mol:5 -141: [17:55:22] Rep: 60 Mol:9 -141: [17:55:22] Rep: 60 Mol:13 -141: [17:55:22] Rep: 60 Mol:17 -141: [17:55:22] Rep: 60 Mol:21 -141: [17:55:22] Rep: 60 Mol:25 -141: [17:55:22] Rep: 60 Mol:29 -148: [17:55:22] Molecule does not have explicit Hs. Consider calling AddHs() -146: [17:55:20] --------------------------------- -146: [17:55:20] test3 -146: -146: [17:55:20] --------------------------------- -146: [17:55:20] test4 -146: -146: [17:55:20] --------------------------------- -146: [17:55:20] test5 -146: -146: [17:55:21] --------------------------------- -146: [17:55:21] test6 -146: -146: [17:55:21] --------------------------------- -146: [17:55:21] test15Dists -146: -146: [17:55:21] --------------------------------- -146: [17:55:21] test Issue 215 -146: -146: [17:55:21] --------------------------------- -146: [17:55:21] testMultipleConfs -146: -146: [17:55:22] --------------------------------- -146: [17:55:22] testMultipleConfsExpTors -146: -146: [17:55:22] --------------------------------- -146: [17:55:22] testIssue227 -146: -146: [17:55:22] --------------------------------- -146: [17:55:22] testIssue236 -146: -146: [17:55:22] --------------------------------- -146: [17:55:22] testOrdering -146: -146: [17:55:22] --------------------------------- -146: [17:55:22] testIssue244 -146: -146: [17:55:22] --------------------------------- -146: [17:55:22] testIssue251 -146: -146: [17:55:22] --------------------------------- -146: [17:55:22] testIssue276 -146: [17:55:22] --------------------------------- -146: [17:55:22] testIssue284 -146: -146: [17:55:22] --------------------------------- -146: [17:55:22] testIssue285 -146: -146: [17:55:22] --------------------------------- -146: [17:55:22] testIssue355 -146: -146: [17:55:22] --------------------------------- -146: [17:55:22] testRandomCoords -146: -146: [17:55:22] --------------------------------- -146: [17:55:22] test sf.net issue 1989539 -146: -146: [17:55:22] --------------------------------- -146: [17:55:22] test sf.net issue 2091864 -146: -146: [17:55:22] --------------------------------- -146: [17:55:22] test constrained embedding -146: -146: [17:55:22] ssd: 0.0752641 -146: [17:55:22] ssd: 0.0659363 -89: =============================================================================== -89: All tests passed (21562 assertions in 3 test cases) -89: -147/236 Test #89: multithreadedSupplierCatchTest ......... Passed 2.52 sec +186: [14:17:45] Non terminal R group defined. To allow set allowNonTerminalRGroups in RGroupDecompositionParameters +186: [14:17:45] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [14:17:45] done +12: .................. +12: ---------------------------------------------------------------------- +12: Ran 18 tests in 8.969s +12: +12: OK +183: [14:17:45] ------------------------------------- +183: [14:17:45] Test2 +160: [14:17:45] unrecognized bond typefile testGithub4238_1.png gave hash 2704600159U not the expected 2623427676U +147: [14:17:46] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +160: file testGithub4323_1.png gave hash 1936109620U not the expected 3075787867U +149/236 Test #181: pyReducedGraphs ........................ Passed 2.29 sec test 189 Start 189: pyRGroupDecomposition 189: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition/Wrap/test_rgroups.py" 189: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap 189: Test timeout computed to be: 1500 -148: [17:55:22] Molecule does not have explicit Hs. Consider calling AddHs() -148: .[17:55:22] Molecule does not have explicit Hs. Consider calling AddHs() -183: [17:55:22] done -183: [17:55:22] ------------------------------------- -183: [17:55:22] Test2 -117: =>start test 2 WHIM custom -117: [17:55:22] test on : 365 molecules done -148/236 Test #98: pyChemReactionEnumerations ............. Passed 2.57 sec +150/236 Test #12: pyBV ................................... Passed 9.53 sec test 190 Start 190: molInterchangeTest1 190: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/molInterchangeTest1 190: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange 190: Test timeout computed to be: 1500 -40: [17:55:22] done: 500000 -40: [17:55:22] Done -190: [17:55:22] test1: basics -184: Randomness seeded to: 4059788630 -184: =============================================================================== -184: All tests passed (171 assertions in 5 test cases) -184: -149/236 Test #184: substructLibraryCatchTest .............. Passed 0.53 sec -test 191 - Start 191: molInterchangeCatchTest - -191: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/molInterchangeCatchTest -191: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange -191: Test timeout computed to be: 1500 -190: [17:55:22] done -190: [17:55:22] test2: basic writing +151: 5013649246 +190: [14:17:46] test1: basics +190: [14:17:46] done +190: [14:17:46] test2: basic writing 190: {"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":"2025.03.1","cipRanks":[0,0]}]}]} 190: {"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":"2025.03.1","cipRanks":[3,1,4,2,0],"cipCodes":[[1,"S"]]}]}]} 190: {"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":"2025.03.1","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]]}]}]} 190: {"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":"2025.03.1","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]]}]}]} -190: [17:55:22] done -190: [17:55:22] test3: writing conformers +190: [14:17:46] done +190: [14:17:46] test3: writing conformers 190: {"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":[[-1.1988,-0.0452],[-0.3332,0.4556],[0.166,1.322],[0.5332,-0.0438],[-2.0652,0.4542],[-0.834,1.3212]]},{"dim":3,"coords":[[0.9554,-0.3743,-0.4679],[-0.3616,-0.1311,-0.0795],[-0.5097,1.6256,0.1706],[-0.5779,-0.792,1.1042],[1.5277,0.1064,0.1628],[-1.0339,-0.4346,-0.8902]]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2025.03.1","cipCodes":[[1,"S"]]},{"name":"partialCharges","generator":"RDKit","formatVersion":10,"generatorVersion":"2025.03.1","values":[-0.352,0.273,-0.055,-0.198,0.215,0.117]}]}]} -190: [17:55:22] done -190: [17:55:22] test4: writing properties +190: [14:17:46] done +190: [14:17:46] test4: writing properties 190: {"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":"2025.03.1","cipRanks":[0,0]}]}]} -190: [17:55:22] done -190: [17:55:22] test5: writing partial charges +190: [14:17:46] done +190: [14:17:46] test5: writing partial charges 190: {"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":"2025.03.1","cipRanks":[0,1]},{"name":"partialCharges","generator":"RDKit","formatVersion":10,"generatorVersion":"2025.03.1","values":[0.5,-0.5]}]}]} -190: [17:55:22] testing parse options -190: [17:55:22] done -190: [17:55:22] testing github #2046: CIPRank values from JSONDataToMols are not unsigned +190: [14:17:46] testing parse options +190: [14:17:46] done +190: [14:17:46] testing github #2046: CIPRank values from JSONDataToMols are not unsigned 190: {"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":"2025.03.1","cipRanks":[1,0,2,4,3,5],"cipCodes":[[4,"S"]],"atomRings":[[0,1,2,3,4]]}]}]} -190: [17:55:22] done -190: [17:55:22] testing 'either' stereochemistry -190: [17:55:22] done -150/236 Test #190: molInterchangeTest1 .................... Passed 0.06 sec +190: [14:17:46] done +190: [14:17:46] testing 'either' stereochemistry +190: [14:17:46] done +151/236 Test #190: molInterchangeTest1 .................... Passed 0.09 sec +test 191 + Start 191: molInterchangeCatchTest + +191: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/molInterchangeCatchTest +191: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange +191: Test timeout computed to be: 1500 +191: Randomness seeded to: 1234347282 +191: [14:17:46] unrecognized bond type 12 set to zero while writing +191: [14:17:46] unrecognized bond type 0 set to zero while writing +191: =============================================================================== +191: All tests passed (125 assertions in 7 test cases) +191: +152/236 Test #191: molInterchangeCatchTest ................ Passed 0.07 sec test 192 Start 192: pyMolInterchange 192: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInterchange/Wrap/testMolInterchange.py" 192: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/Wrap 192: Test timeout computed to be: 1500 -186: [17:55:22] Non terminal R group defined. To allow set allowNonTerminalRGroups in RGroupDecompositionParameters -148: [17:55:22] Molecule does not have explicit Hs. Consider calling AddHs() -141: [17:55:22] Rep: 60 Mol:2 -186: [17:55:22] WARNING: not removing hydrogen atom with dummy atom neighbors -141: [17:55:22] Rep: 60 Mol:6 -141: [17:55:22] Rep: 60 Mol:10 -146: [17:55:22] --------------------------------- -146: [17:55:22] test sf.net issue 2091974 -146: -146: [17:55:22] --------------------------------- -146: [17:55:22] test sf.net issue 2835784 -146: -146: [17:55:22] --------------------------------- -146: [17:55:22] test sf.net issue 3019283 -146: -146: [17:55:22] --------------------------------- -146: [17:55:22] test sf.net issue 3238580 -146: -146: [17:55:22] --------------------------------- -146: [17:55:22] test sf.net issue 3483968 -146: -146: [17:55:22] --------------------------------- -146: [17:55:22] test github issue 55 -146: -146: [17:55:22] --------------------------------- -146: [17:55:22] test1 -146: -146: [17:55:22] --------------------------------- -146: [17:55:22] test multi-threading -146: -146: building molecules -191: Randomness seeded to: 941414203 -191: [17:55:22] unrecognized bond type 12 set to zero while writing -191: [17:55:22] unrecognized bond type 0 set to zero while writing -141: [17:55:22] Rep: 60 Mol:14 -141: [17:55:22] Rep: 60 Mol:18 -141: [17:55:22] Rep: 60 Mol:22 -141: [17:55:22] Rep: 60 Mol:26 -191: =============================================================================== -191: All tests passed (125 assertions in 7 test cases) -191: -141: [17:55:22] Rep: 60 Mol:30 -151/236 Test #191: molInterchangeCatchTest ................ Passed 0.05 sec +148: [14:17:46] Molecule does not have explicit Hs. Consider calling AddHs() +184: Randomness seeded to: 3303982592 +184: =============================================================================== +184: All tests passed (171 assertions in 5 test cases) +184: +153/236 Test #184: substructLibraryCatchTest .............. Passed 1.86 sec test 193 Start 193: testSLNParse 193: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/testSLNParse 193: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse 193: Test timeout computed to be: 1500 -146: generating reference data -141: [17:55:22] Rep: 80 Mol:0 -141: [17:55:22] Rep: 80 Mol:4 -141: [17:55:22] Rep: 80 Mol:8 -141: [17:55:22] Rep: 80 Mol:12 -141: [17:55:22] Rep: 80 Mol:16 -141: [17:55:22] Rep: 80 Mol:20 -141: [17:55:22] Rep: 80 Mol:24 -141: [17:55:22] Rep: 80 Mol:28 -40: [17:55:22] Testing hanoi with a functor. -40: [17:55:22] Done -40: [17:55:22] Testing basic partition refinement. -40: [17:55:22] Done -40: [17:55:22] Testing partition refinement with neighbors. -40: [17:55:22] Done -40: [17:55:22] testing canonicalization via tie breaking. -40: [17:55:22] Done -40: [17:55:22] testing canonicalization using the wrapper. +147: [14:17:46] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +183: [14:17:46] done +183: [14:17:46] ------------------------------------- +183: [14:17:46] Test3 (stereo options) 193: Atoms: 193: 0 6 C chg: 1 deg: 5 exp: N/A imp: 0 hyb: 193: 1 1 H chg: 0 deg: 1 exp: N/A imp: N/A hyb: @@ -29746,353 +29738,213 @@ 193: 2 0->3 order: 1 193: 3 0->4 order: 1 193: 4 0->5 order: 1 -193: [17:55:22] SLN Parse Error: syntax error while parsing: CH4[I=13] -193: [17:55:22] Failed parsing SLN 'CH4[I=13]' -193: [17:55:22] SLN Parser error: Atom ID 1 appears *after* its ring closure. -193: [17:55:22] SLN Parser error: Ring closure 1 does not have a corresponding opener. -193: [17:55:22] SLN Parse Error: syntax error while parsing: CH2(C@1H2)CH2(CH2CH2C[1]H2) -193: [17:55:22] Failed parsing SLN 'CH2(C@1H2)CH2(CH2CH2C[1]H2)' -193: [17:55:22] SLN Parse Error: syntax error while parsing: CH2(CH2[1])CH2(CH2CH2CH2@1) -193: [17:55:22] Failed parsing SLN 'CH2(CH2[1])CH2(CH2CH2CH2@1)' -40: [17:55:22] Done -40: [17:55:22] testing some specific ordering problems -193: [17:55:22] SLN Parse Error: syntax error while parsing: CH4 fff -193: [17:55:22] Failed parsing SLN 'CH4 fff' -40: [17:55:22] Finished -40: [17:55:22] testing chiral invariants. -40: [17:55:22] Finished -40: [17:55:22] testing unique ranks in w.r.t. renumbering. -193: [17:55:22] SLN Parse Error: syntax error while parsing: C[charge=+1] foo -193: [17:55:22] Failed parsing SLN 'C[charge=+1] foo' -193: [17:55:22] Query property 'is' ignored on non-query atom -193: [17:55:22] Query property 'is' ignored on non-query atom -152/236 Test #193: testSLNParse ........................... Passed 0.09 sec +193: [14:17:46] SLN Parse Error: syntax error while parsing: CH4[I=13] +193: [14:17:46] Failed parsing SLN 'CH4[I=13]' +193: [14:17:46] SLN Parser error: Atom ID 1 appears *after* its ring closure. +193: [14:17:46] SLN Parser error: Ring closure 1 does not have a corresponding opener. +193: [14:17:46] SLN Parse Error: syntax error while parsing: CH2(C@1H2)CH2(CH2CH2C[1]H2) +193: [14:17:46] Failed parsing SLN 'CH2(C@1H2)CH2(CH2CH2C[1]H2)' +193: [14:17:46] SLN Parse Error: syntax error while parsing: CH2(CH2[1])CH2(CH2CH2CH2@1) +193: [14:17:46] Failed parsing SLN 'CH2(CH2[1])CH2(CH2CH2CH2@1)' +193: [14:17:46] SLN Parse Error: syntax error while parsing: CH4 fff +193: [14:17:46] Failed parsing SLN 'CH4 fff' +193: [14:17:46] SLN Parse Error: syntax error while parsing: C[charge=+1] foo +193: [14:17:46] Failed parsing SLN 'C[charge=+1] foo' +193: [14:17:46] Query property 'is' ignored on non-query atom +193: [14:17:46] Query property 'is' ignored on non-query atom +154/236 Test #193: testSLNParse ........................... Passed 0.13 sec test 194 Start 194: pySLNParse 194: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/SLNParse/Wrap/testSLN.py" 194: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap 194: Test timeout computed to be: 1500 -188: Randomness seeded to: 3246768151 -188: =============================================================================== -188: All tests passed (1475 assertions in 14 test cases) -188: -153/236 Test #188: rgroupCatchTests ....................... Passed 0.46 sec +169: ......... +169: ---------------------------------------------------------------------- +169: Ran 9 tests in 4.097s +169: +169: OK +147: [14:17:46] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +155/236 Test #169: pyMMPA ................................. Passed 4.55 sec test 195 Start 195: pyGraphMolWrap 195: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/rough_test.py" 195: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap 195: Test timeout computed to be: 1500 -160: file testHandDrawn-5a.svg gave hash 3327818543U not the expected 1567781555U -160: [17:55:22] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [17:55:22] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. -40: [17:55:22] Finished -40: [17:55:22] testing mol fragments. -40: [17:55:22] Finished -40: [17:55:22] testing protein round-tripping. -148: [17:55:22] Molecule does not have explicit Hs. Consider calling AddHs() -141: [17:55:22] Rep: 80 Mol:1 -141: [17:55:22] Rep: 80 Mol:5 -141: [17:55:22] Rep: 80 Mol:9 -141: [17:55:22] Rep: 80 Mol:13 -141: [17:55:22] Rep: 80 Mol:17 -141: [17:55:22] Rep: 80 Mol:21 -141: [17:55:22] Rep: 80 Mol:25 -141: [17:55:22] Rep: 80 Mol:29 -160: file testHandDrawn-5b.svg gave hash 2125846125U not the expected 66354106U -160: [17:55:22] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [17:55:22] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. -183: [17:55:22] done -183: [17:55:22] ------------------------------------- -183: [17:55:22] Test3 (stereo options) -125: Warning: Atom Count for residue GLU150A does not match expected count -141: [17:55:22] Rep: 80 Mol:2 -141: [17:55:22] Rep: 80 Mol:6 -141: [17:55:22] Rep: 80 Mol:10 -141: [17:55:22] Rep: 80 Mol:14 -141: [17:55:22] Rep: 80 Mol:18 -141: [17:55:22] Rep: 80 Mol:22 -141: [17:55:22] Rep: 80 Mol:26 -141: [17:55:22] Rep: 80 Mol:30 -160: file testHandDrawn-5.png gave hash 2441005674U not the expected 828378555U -125: Warning: Atom Count for residue ASN157A does not match expected count -163: MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds -163: Time elapsed 0.000 seconds -163: -163: test32() -163: 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 -163: Time elapsed 0.122 seconds -163: -163: test190() -163: 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 -163: Time elapsed 0.018 seconds -163: -163: test3() -163: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6]-[#6](=[#8])-[#7]-[#6]-[#6]-[#6]-[#6] 14 atoms, 14 bonds -163: Time elapsed 0.017 seconds -163: -163: testSimpleFast() -163: 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 -163: Time elapsed 0.117 seconds -163: -163: testSimple() -163: MCS: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds -163: Time elapsed 0.094 seconds -163: MCS MatchFusedRings: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds -163: Time elapsed 0.131 seconds -163: MCS MatchFusedRingsStrict: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds -163: Time elapsed 0.169 seconds -163: -163: testSegFault() -163: MCS: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds -163: Time elapsed 0.010 seconds -163: MCS MatchFusedRings: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds -163: Time elapsed 0.014 seconds -163: 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 -163: Time elapsed 0.018 seconds -163: -163: testThreshold() -163: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds -163: Time elapsed 0.000 seconds -163: -163: testRing1() -163: 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 -163: Time elapsed 0.466 seconds -163: 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 -163: Time elapsed 0.370 seconds -163: 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 -163: Time elapsed 0.428 seconds -163: -163: testAtomCompareIsotopes() -163: MCS: [0*]-[0*]-[13*] 3 atoms, 2 bonds -163: Time elapsed 0.000 seconds -163: -163: testAtomCompareAnyAtom() -163: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#7,#8,#9,#17] 7 atoms, 7 bonds -163: Time elapsed 0.000 seconds -163: -163: testAtomCompareAnyAtom() -163: MCS: [#6]1-,:[#6]-,:[#6]-,:[#6]-,:[#6]-,:[#6]-,:1=,-[#6,#7,#8,#9,#17] 7 atoms, 7 bonds -163: Time elapsed 0.000 seconds -163: -163: testAtomCompareAnyAtom() -163: MCS: [#1]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#8] 8 atoms, 8 bonds -163: Time elapsed 0.000 seconds -163: -163: testAtomCompareAnyAtom() -163: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#8] 7 atoms, 7 bonds -163: Time elapsed 0.000 seconds -163: -163: testJnk1LigandsDistance() -163: 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 -160: file testBrackets-5a.svg gave hash 279553678U not the expected 1447240271U -163: Time elapsed 0.016 seconds -163: 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 +183: [14:17:46] Done (stereo options) +183: [14:17:46] ------------------------------------- +183: [14:17:46] Test4 (trusted smiles) +146: [14:17:40] --------------------------------- +146: [14:17:40] test3 +146: +146: [14:17:40] --------------------------------- +146: [14:17:40] test4 +146: +146: [14:17:40] --------------------------------- +146: [14:17:40] test5 +146: +146: [14:17:46] --------------------------------- +146: [14:17:46] test6 +146: +146: [14:17:46] --------------------------------- +146: [14:17:46] test15Dists +146: +146: [14:17:46] --------------------------------- +146: [14:17:46] test Issue 215 +146: +146: [14:17:46] --------------------------------- +146: [14:17:46] testMultipleConfs +146: +146: [14:17:46] --------------------------------- +146: [14:17:46] testMultipleConfsExpTors +146: +146: [14:17:46] --------------------------------- +146: [14:17:46] testIssue227 +146: +146: [14:17:46] --------------------------------- +146: [14:17:46] testIssue236 +146: +146: [14:17:46] --------------------------------- +146: [14:17:46] testOrdering +146: +146: [14:17:46] --------------------------------- +146: [14:17:46] testIssue244 +146: +146: [14:17:46] --------------------------------- +146: [14:17:46] testIssue251 +146: +146: [14:17:46] --------------------------------- +146: [14:17:46] testIssue276 +146: [14:17:46] --------------------------------- +146: [14:17:46] testIssue284 +146: +146: [14:17:46] --------------------------------- +146: [14:17:46] testIssue285 +146: +146: [14:17:46] --------------------------------- +146: [14:17:46] testIssue355 +146: +146: [14:17:46] --------------------------------- +146: [14:17:46] testRandomCoords +146: +146: [14:17:46] --------------------------------- +146: [14:17:46] test sf.net issue 1989539 +146: +146: [14:17:46] --------------------------------- +146: [14:17:46] test sf.net issue 2091864 +146: +146: [14:17:46] --------------------------------- +146: [14:17:46] test constrained embedding +146: +146: [14:17:46] ssd: 0.0752641 +146: [14:17:46] ssd: 0.0659363 +148: [14:17:46] Molecule does not have explicit Hs. Consider calling AddHs() +160: file testGithub4323_3.png gave hash 1732257634U not the expected 381907253U +160: [14:17:46] FIELDDISP info not found for DAT SGroup which isn't associated with an atom. SGroup will not be rendered. 192: .. 192: ---------------------------------------------------------------------- -192: Ran 2 tests in 0.014s +192: Ran 2 tests in 0.012s 192: 192: OK -148: [17:55:22] Molecule does not have explicit Hs. Consider calling AddHs() -154/236 Test #192: pyMolInterchange ....................... Passed 0.44 sec +156/236 Test #192: pyMolInterchange ....................... Passed 0.67 sec test 196 Start 196: pyTestConformerWrap 196: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/testConformer.py" 196: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap 196: Test timeout computed to be: 1500 -126: Warning: Atom Count for residue GLU150A does not match expected count -117: =>start test 1 WHIM custom 194: .. 194: ---------------------------------------------------------------------- -194: Ran 2 tests in 0.012s +194: Ran 2 tests in 0.029s 194: 194: OK -160: file testPositionVariation-1b.svg gave hash 3055422087U not the expected 3269244452U -117: [17:55:22] test on : 365 molecules done -183: [17:55:22] Done (stereo options) -183: [17:55:22] ------------------------------------- -183: [17:55:22] Test4 (trusted smiles) -155/236 Test #194: pySLNParse ............................. Passed 0.40 sec +40: [14:17:46] Finished +40: [14:17:46] testing stability w.r.t. renumbering. +146: [14:17:46] --------------------------------- +146: [14:17:46] test sf.net issue 2091974 +146: +146: [14:17:46] --------------------------------- +146: [14:17:46] test sf.net issue 2835784 +146: +146: [14:17:46] --------------------------------- +146: [14:17:46] test sf.net issue 3019283 +146: +146: [14:17:46] --------------------------------- +146: [14:17:46] test sf.net issue 3238580 +146: +146: [14:17:46] --------------------------------- +146: [14:17:46] test sf.net issue 3483968 +146: +146: [14:17:46] --------------------------------- +146: [14:17:46] test github issue 55 +146: +146: [14:17:46] --------------------------------- +146: [14:17:46] test1 +146: +146: [14:17:46] --------------------------------- +146: [14:17:46] test multi-threading +146: +146: building molecules +183: [14:17:46] Done (trusted smiles) +183: [14:17:46] ------------------------------------- +183: [14:17:46] Testing C++ docs +183: [14:17:46] Done (C++ doc tests) +183: [14:17:46] ------------------------------------- +183: [14:17:46] Testing C++ ring query: PatternHolder +183: [14:17:46] Done (C++ ring query tests) +183: [14:17:46] ------------------------------------- +183: [14:17:46] Testing C++ ring query: TautomerPatternHolder +183: [14:17:46] Done (C++ ring query tests) +183: [14:17:46] ------------------------------------- +183: [14:17:46] Add Patterns +29: Checking against /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +147: [14:17:47] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +146: generating reference data +147: [14:17:47] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +157/236 Test #194: pySLNParse ............................. Passed 0.59 sec test 197 Start 197: pyTestTrajectory 197: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/testTrajectory.py" 197: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap 197: Test timeout computed to be: 1500 -163: Time elapsed 0.002 seconds -163: -163: test18() -163: 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 -163: 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 -163: Time elapsed 0.007 seconds -163: -163: test504() -163: 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 -163: 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 -163: Time elapsed 0.096 seconds -163: MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds -163: Time elapsed 0.001 seconds -163: 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 -163: Time elapsed 0.029 seconds -163: Query Cc1c(F)c(N2CCNC(C)C2)cc2c1c(=O)c(C(=O)O)cn2C1CC1 26(26) atoms, 29(28) bonds -163: 1 Seeds:1 MCS 25 atoms, 28 bonds for 0.0007 seconds. bond[0]=6 -163: STATISTICS: -163: Total Growing Steps = 1, MCS found on 1 step, for 0.0007 seconds -163: Initial Seeds = 1, Mismatched 0 -163: Inspected Seeds = 2 -163: Rejected by BestSize = 0 -163: IndividualBondExcluded = 0 -163: MatchCheck Seeds = 2 -163: MatchCalls = 2 -163: MatchFound = 1 -163: fastMatchCalls = 1 -163: fastMatchFound = 0 -163: slowMatchCalls = 2 -163: slowMatchFound = 1 -163: DupCacheFound = 0 0 matched, 0 mismatched -163: HashCache size = 1 keys -163: HashCache size = 1 entries -163: FindHashInCache = 2 -163: HashFoundInCache= 0 -163: ExactMatchCalls = 0 -163: ExactMatchFound = 0 -163: Time elapsed 0.001 seconds -163: query=OCCl SubstructMatch(useChirality=false) res =1 size=3 -163: query=OCCl SubstructMatch(useChirality=true ) res =1 size=3 -163: test target = O[C@H](F)CCl query = C(F)C useChirality = 0 -163: res sub = 1 size=3 -163: MCS: [#6](-[#9])-[#6] 3 atoms, 2 bonds -163: test target = O[C@H](F)CCl query = C(F)C useChirality = 1 -163: res sub = 1 size=3 -163: MCS: [#6](-[#9])-[#6] 3 atoms, 2 bonds -163: test target = CC[C@H](F)Cl query = CCC useChirality = 0 -163: res sub = 1 size=3 -163: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds -163: test target = CC[C@H](F)Cl query = CCC useChirality = 1 -163: res sub = 1 size=3 -163: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds -163: test target = CCC(F)Cl query = CC useChirality = 0 -163: res sub = 1 size=2 -163: MCS: [#6]-[#6] 2 atoms, 1 bonds -163: test target = CCC(F)Cl query = CC useChirality = 1 -163: res sub = 1 size=2 -163: MCS: [#6]-[#6] 2 atoms, 1 bonds -163: test target = C[C@H](F)CCl query = C[C@H](F)C useChirality = 0 -163: res sub = 1 size=4 -163: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -163: test target = C[C@H](F)CCl query = C[C@H](F)C useChirality = 1 -163: res sub = 1 size=4 -163: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -163: test target = C[C@H](F)CCl query = C[C@@H](F)C useChirality = 0 -163: res sub = 1 size=4 -163: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -163: test target = C[C@H](F)CCl query = C[C@@H](F)C useChirality = 1 -163: res sub = 1 size=4 -163: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -163: test target = O[C@H](F)CCl query = CC(F)C useChirality = 0 -163: res sub = 0 size=0 -163: MCS: [#6]-[#6]-[#9] 3 atoms, 2 bonds -163: test target = O[C@H](F)CCl query = CC(F)C useChirality = 1 -163: res sub = 0 size=0 -163: MCS: [#6]-[#6]-[#9] 3 atoms, 2 bonds -163: test target = O[C@H](F)CCl query = OC(F)C useChirality = 0 -163: res sub = 1 size=4 -163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -163: test target = O[C@H](F)CCl query = OC(F)C useChirality = 1 -163: res sub = 1 size=4 -163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -163: test target = O[C@H](F)CCl query = O[C@H](F)C useChirality = 0 -163: res sub = 1 size=4 -163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -163: test target = O[C@H](F)CCl query = O[C@H](F)C useChirality = 1 -163: res sub = 1 size=4 -163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -163: test target = O[C@H](F)CCl query = O[C@@H](F)C useChirality = 0 -163: res sub = 1 size=4 -163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -163: test target = O[C@H](F)CCl query = O[C@@H](F)C useChirality = 1 -163: res sub = 0 size=0 -163: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds -163: test target = OC(F)CCl query = OC(F)C useChirality = 0 -163: res sub = 1 size=4 -163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -163: test target = OC(F)CCl query = OC(F)C useChirality = 1 -163: res sub = 1 size=4 -163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -163: test target = OC(F)CCl query = O[C@H](F)C useChirality = 0 -163: res sub = 1 size=4 -163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -163: test target = OC(F)CCl query = O[C@H](F)C useChirality = 1 -143: [17:55:22] done -143: [17:55:22] ------------------------------------- -143: [17:55:22] Test UFF multithreading2 -163: res sub = 0 size=0 -163: MCS: [#9] 1 atoms, 0 bonds -163: test target = OC(F)CCl query = O[C@@H](F)C useChirality = 0 -163: res sub = 1 size=4 -163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -163: test target = OC(F)CCl query = O[C@@H](F)C useChirality = 1 -163: res sub = 0 size=0 -163: MCS: [#9] 1 atoms, 0 bonds -163: test target = O[C@H](F)CCl query = O[C@H]C useChirality = 0 -163: res sub = 1 size=3 -163: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds -163: test target = O[C@H](F)CCl query = O[C@H]C useChirality = 1 -163: res sub = 1 size=3 -163: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds -163: test target = O[C@H](F)CCl query = O[C@@H]C useChirality = 0 -163: res sub = 1 size=3 -163: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds -163: test target = O[C@H](F)CCl query = O[C@@H]C useChirality = 1 -163: res sub = 1 size=3 -163: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds -163: -163: 0. <<<<<<<<< actual MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds >>>>>>> -163: test target = CC[C@H](F)Cl query = CC[C@H] useChirality = 0 -163: res sub = 1 size=3 -163: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds -163: test target = CC[C@H](F)Cl query = CC[C@H] useChirality = 1 -163: res sub = 1 size=3 -163: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds -163: done -151: 2338499801 -126: Warning: Atom Count for residue ASN157A does not match expected count -141: [17:55:22] done -141: [17:55:22] ------------------------------------- -141: [17:55:22] Test MMFF multithreading2 -160: [17:55:22] unrecognized bond typefile testGithub4238_1.png gave hash 2704600159U not the expected 2623427676U -160: file testGithub4323_1.png gave hash 1936109620U not the expected 3075787867U -183: [17:55:23] Done (trusted smiles) -183: [17:55:23] ------------------------------------- -183: [17:55:23] Testing C++ docs -183: [17:55:23] Done (C++ doc tests) -183: [17:55:23] ------------------------------------- -183: [17:55:23] Testing C++ ring query: PatternHolder -183: [17:55:23] Done (C++ ring query tests) -183: [17:55:23] ------------------------------------- -183: [17:55:23] Testing C++ ring query: TautomerPatternHolder -183: [17:55:23] Done (C++ ring query tests) -183: [17:55:23] ------------------------------------- -183: [17:55:23] Add Patterns -156/236 Test #42: resMolSupplierTest ..................... Passed 6.20 sec +188: Randomness seeded to: 2103461638 +188: =============================================================================== +188: All tests passed (1475 assertions in 14 test cases) +188: +158/236 Test #188: rgroupCatchTests ....................... Passed 1.22 sec test 198 Start 198: pyTestSGroups 198: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/testSGroups.py" 198: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap 198: Test timeout computed to be: 1500 -148: [17:55:23] Molecule does not have explicit Hs. Consider calling AddHs() -143: [17:55:23] done -143: [17:55:23] ------------------------------------- -143: [17:55:23] Test UFF multithreading3 -141: [17:55:23] done -141: [17:55:23] ------------------------------------- -141: [17:55:23] Test MMFF multithreading3 -160: file testGithub4323_3.png gave hash 1732257634U not the expected 381907253U -160: [17:55:23] FIELDDISP info not found for DAT SGroup which isn't associated with an atom. SGroup will not be rendered. -197: [17:55:23] +98: . +98: ---------------------------------------------------------------------- +98: Ran 11 tests in 7.659s +98: +98: OK +98: True +98: == CartesianProductStrategy CartesianProductStrategy +98: 197 out of 300 +98: 0 6 out of 10 +98: 1 3 out of 5 +98: 2 4 out of 6 +98: 198 out of 300 +98: 0 10 out of 10 +98: 1 5 out of 5 +98: 2 6 out of 6 +98: Skipped 10000000 in 0.30815577507019043 seconds +98: Skipped 10000000 in 3.6240501403808594 seconds +98: Skipped 10000000 in 2.3353474140167236 seconds +147: [14:17:47] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +125: Warning: Atom Count for residue GLU150A does not match expected count +40: [14:17:47] Finished +40: [14:17:47] testing smiles round-tripping. +173: Randomness seeded to: 423180356 +173: [14:17:47] Writing the enumerated file may take quite some time and result in a large file. +197: [14:17:47] 197: 197: **** 197: Pre-condition Violation @@ -30106,23 +29958,23 @@ 197: 2# RDKit::Trajectory::addConformersToMol(RDKit::ROMol&, int, int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 197: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 5# 0x00007F488FE1B62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x00007F891D7B462C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 11# 0x00007F488D9B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 12# 0x00007F488D9B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 13# 0x00007F488D9B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 14# 0x00007F488D9B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 15# 0x00007F488D9B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 11# 0x00007F891B3B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 12# 0x00007F891B3B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 13# 0x00007F891B3B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 14# 0x00007F891B3B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 15# 0x00007F891B3B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 21# 0x00007F488FE183C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 21# 0x00007F891D7B13C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 22# _PyObject_MakeTpCall in /usr/bin/python3 197: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 24# 0x00000000005CD3C9 in /usr/bin/python3 @@ -30154,13 +30006,13 @@ 197: 50# 0x00000000006B921E in /usr/bin/python3 197: 51# Py_RunMain in /usr/bin/python3 197: 52# Py_BytesMain in /usr/bin/python3 -197: 53# 0x00007F48905C4CA8 in /lib/x86_64-linux-gnu/libc.so.6 +197: 53# 0x00007F891DF5DCA8 in /lib/x86_64-linux-gnu/libc.so.6 197: 54# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 197: 55# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: .[17:55:23] +197: .[14:17:47] 197: 197: **** 197: Pre-condition Violation @@ -30174,23 +30026,23 @@ 197: 2# RDKit::Trajectory::addConformersToMol(RDKit::ROMol&, int, int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 197: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 5# 0x00007F488FE1B62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x00007F891D7B462C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 11# 0x00007F488D9B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 12# 0x00007F488D9B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 13# 0x00007F488D9B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 14# 0x00007F488D9B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 15# 0x00007F488D9B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 11# 0x00007F891B3B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 12# 0x00007F891B3B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 13# 0x00007F891B3B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 14# 0x00007F891B3B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 15# 0x00007F891B3B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 21# 0x00007F488FE183C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 21# 0x00007F891D7B13C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 22# _PyObject_MakeTpCall in /usr/bin/python3 197: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 24# 0x00000000005CD3C9 in /usr/bin/python3 @@ -30222,129 +30074,88 @@ 197: 50# 0x00000000006B921E in /usr/bin/python3 197: 51# Py_RunMain in /usr/bin/python3 197: 52# Py_BytesMain in /usr/bin/python3 -197: 53# 0x00007F48905C4CA8 in /lib/x86_64-linux-gnu/libc.so.6 +197: 53# 0x00007F891DF5DCA8 in /lib/x86_64-linux-gnu/libc.so.6 197: 54# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 197: 55# _start in /usr/bin/python3 197: ---------- 197: **** 197: -40: [17:55:23] Finished -40: [17:55:23] testing stability w.r.t. renumbering. -172: .... -172: ---------------------------------------------------------------------- -172: Ran 14 tests in 2.345s -172: -172: OK -143: [17:55:23] done -143: [17:55:23] ------------------------------------- -143: [17:55:23] Testing GitHubIssue62. -195: ..............[17:55:23] SMARTS Parse Error: syntax error while parsing: fiib -195: [17:55:23] SMARTS Parse Error: Failed parsing SMARTS 'fiib' for input: 'fiib' -40: [17:55:23] Finished -40: [17:55:23] testing smiles round-tripping. -143: [17:55:23] beta-lactam 39.6387 -143: [17:55:23] cyclopropanone 174.698 -143: [17:55:23] aziridine 337.986 -143: [17:55:23] aziridinone 115.248 -148: [17:55:23] Molecule does not have explicit Hs. Consider calling AddHs() -122: =>start test GETAWAY -143: [17:55:23] isobutene 2.48217 -122: [17:55:23] test on : 365 molecules done -141: [17:55:23] done -141: [17:55:23] ------------------------------------- -141: [17:55:23] Testing github 162: Incorrect SMILES after MMFF parameterization . -141: [17:55:23] done -141: [17:55:23] ------------------------------------- -141: [17:55:23] Testing github 224: crash during MMFF parameterization . -157/236 Test #122: testGETAWAY ............................ Passed 3.81 sec +143: [14:17:47] done +143: [14:17:47] ------------------------------------- +143: [14:17:47] Test UFF multithreading2 +159/236 Test #98: pyChemReactionEnumerations ............. Passed 9.18 sec test 199 Start 199: pyTestThreads 199: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/testThreads.py" 199: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap 199: Test timeout computed to be: 1500 +69: [14:17:47] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +69: [14:17:47] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +69: [14:17:47] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +69: [14:17:47] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +69: [14:17:47] deprecated group abbreviation ignored on line 24 +160: file testFlexiCanvas.2a.png gave hash 1389326866U not the expected 2609920321U +160: file testFlexiCanvas.2b.png gave hash 614693993U not the expected 3615599154U +69: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] +69: [14:17:47] +69: +69: **** +69: Post-condition Violation +69: Element 'Mv' not found +69: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h +69: Failed Expression: anum > -1 +69: ---------- +69: Stacktrace: +69: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +69: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +69: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 3# 0x00007FECAF2C8531 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 4# 0x00007FECAF2D1DFA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 5# 0x00007FECAF2D217D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 6# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 8# RDKit::v2::FileParsers::MolFromMolFile(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 9# 0x000055AD5A891C15 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 10# 0x000055AD5A8F8372 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 11# 0x000055AD5A8789A3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 12# 0x00007FECAE833CA8 in /lib/x86_64-linux-gnu/libc.so.6 +69: 13# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +69: 14# 0x000055AD5A878AD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: ---------- +69: **** +69: +125: Warning: Atom Count for residue ASN157A does not match expected count +198: ............. +198: ---------------------------------------------------------------------- +198: Ran 13 tests in 0.027s +198: +198: OK +198: Testing SubstanceGroups wrapper +29: All 191 tests passed 196: ...... 196: ---------------------------------------------------------------------- -196: Ran 6 tests in 0.064s +196: Ran 6 tests in 0.015s 196: 196: OK -143: [17:55:23] acetone 1.91788 -141: [17:55:23] done -141: [17:55:23] ------------------------------------- -141: [17:55:23] Testing github6728: crash due to missing stretch-bend params. -143: [17:55:23] cyclopentanone 10.1648 -143: [17:55:23] cyclopropene 99.4921 -158/236 Test #141: testMMFFForceFieldHelpers .............. Passed 3.48 sec -143: [17:55:23] cyclobutene 41.0156 +160: file testFlexiCanvas.3.svg gave hash 236661785U not the expected 3544316588U +122: =>start test GETAWAY +122: [14:17:47] test on : 365 molecules done +160/236 Test #122: testGETAWAY ............................ Passed 8.78 sec test 200 Start 200: pyTestMultithreadedMolSupplier 200: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/testMultithreadedMolSupplier.py" 200: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap 200: Test timeout computed to be: 1500 -143: [17:55:23] cyclopropane 267.236 -143: [17:55:23] gamma-lactam 15.7471 -198: ............. -198: ---------------------------------------------------------------------- -198: Ran 13 tests in 0.032s -198: -198: OK -198: Testing SubstanceGroups wrapper -195: ....[17:55:23] ERROR: Problems encountered parsing data fields -195: [17:55:23] ERROR: moving to the beginning of the next molecule -195: [17:55:23] ERROR: Problems encountered parsing data fields -195: [17:55:23] ERROR: moving to the beginning of the next molecule -195: [17:55:23] Spurious data before the first property will be ignored -195: [17:55:23] Property will be truncated after the first blank line -195: [17:55:23] Property will be truncated after the first blank line -195: [17:55:23] Property will be truncated after the first blank line -195: [17:55:23] ERROR: Problems encountered parsing data fields -195: [17:55:23] ERROR: moving to the beginning of the next molecule -195: [17:55:23] ERROR: Problems encountered parsing data fields -195: [17:55:23] ERROR: moving to the beginning of the next molecule -195: [17:55:23] Spurious data before the first property will be ignored -195: [17:55:23] Property will be truncated after the first blank line -195: [17:55:23] Property will be truncated after the first blank line -195: [17:55:23] Property will be truncated after the first blank line -195: [17:55:23] ERROR: Problems encountered parsing data fields -195: [17:55:23] ERROR: moving to the beginning of the next molecule -195: [17:55:23] Property will be truncated after the first blank line -195: [17:55:23] ERROR: Problems encountered parsing data fields -195: [17:55:23] ERROR: moving to the beginning of the next molecule -195: [17:55:23] Property will be truncated after the first blank line -143: [17:55:23] trans-2,3-diphenylcyclopropan-1-one 203.398 -159/236 Test #172: pyRascalMCES ........................... Passed 2.85 sec +161/236 Test #196: pyTestConformerWrap .................... Passed 0.66 sec test 201 Start 201: pyTestPropertyLists 201: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/testPropertyLists.py" 201: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap 201: Test timeout computed to be: 1500 -195: .[17:55:23] SMILES Parse Error: syntax error while parsing: fail -195: [17:55:23] SMILES Parse Error: check for mistakes around position 1: -195: [17:55:23] fail -195: [17:55:23] ^ -195: [17:55:23] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' -195: [17:55:23] ERROR: Smiles parse error on line 2 -195: [17:55:23] ERROR: Cannot create molecule from : 'fail' -195: >>> This may result in an infinite loop. It should finish almost instantly -195: <<< OK, it finished. -173: Randomness seeded to: 858805632 -173: [17:55:23] Writing the enumerated file may take quite some time and result in a large file. -160/236 Test #198: pyTestSGroups .......................... Passed 0.53 sec -test 202 - Start 202: pyCDXMLTest - -202: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/test_cdxml.py" -202: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap -202: Test timeout computed to be: 1500 -143: [17:55:23] cis-2,3-diphenylcyclopropan-1-one 206.852 -195: ............[17:55:23] Explicit valence for atom # 1 C, 5, is greater than permitted -143: [17:55:23] 2,3-diphenylcyclopropa-2-en-1-one 20.0443 -195: ......[17:55:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -195: [17:55:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [17:55:23] cyclopropylidencyclobutane 218.879 -197: .[17:55:23] +197: .[14:17:47] 197: 197: **** 197: Range Error @@ -30359,23 +30170,23 @@ 197: 3# RDKit::getSnapshot_wrap(RDKit::Trajectory*, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 4# boost::python::objects::caller_py_function_impl, boost::mpl::vector3 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 6# 0x00007F488FE1B62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 6# 0x00007F891D7B462C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 12# 0x00007F488D9B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 13# 0x00007F488D9B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 14# 0x00007F488D9B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 15# 0x00007F488D9B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 16# 0x00007F488D9B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 12# 0x00007F891B3B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 13# 0x00007F891B3B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 14# 0x00007F891B3B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 15# 0x00007F891B3B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 16# 0x00007F891B3B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 20# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 21# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 22# 0x00007F488FE183C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 22# 0x00007F891D7B13C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 23# _PyObject_MakeTpCall in /usr/bin/python3 197: 24# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 25# 0x00000000005CD3C9 in /usr/bin/python3 @@ -30407,16 +30218,13 @@ 197: 51# 0x00000000006B921E in /usr/bin/python3 197: 52# Py_RunMain in /usr/bin/python3 197: 53# Py_BytesMain in /usr/bin/python3 -197: 54# 0x00007F48905C4CA8 in /lib/x86_64-linux-gnu/libc.so.6 +197: 54# 0x00007F891DF5DCA8 in /lib/x86_64-linux-gnu/libc.so.6 197: 55# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 197: 56# _start in /usr/bin/python3 197: ---------- 197: **** 197: -195: [17:55:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -195: [17:55:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -195: .inWedges: [H]C12C3([H])C4([H])C1([H])C1([H])C2([H])C3([H])C41[H] |(-0.612,-0.6446,0.635;0.0021,-0.0041,0.002;-0.0187,1.5258,0.0104;-0.6498,2.1424,0.6504;1.5111,1.5466,-0.0041;2.1372,2.1804,0.624;1.5319,0.0168,-0.0125;2.175,-0.6067,0.6086;1.5173,0.025,-1.5424;2.1484,-0.5936,-2.1805;-0.0125,0.0041,-1.5279;-0.6405,-0.6297,-2.154;-0.0333,1.534,-1.5195;-0.6783,2.1574,-2.1387;1.4965,1.5548,-1.534;2.1106,2.1972,-2.1651)| -197: .[17:55:23] +197: .[14:17:47] 197: 197: **** 197: Pre-condition Violation @@ -30430,23 +30238,23 @@ 197: 2# RDKit::readAmberTrajectory(std::__cxx11::basic_string, std::allocator > const&, RDKit::Trajectory&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 197: 3# boost::python::objects::caller_py_function_impl, std::allocator > const&, RDKit::Trajectory&), boost::python::default_call_policies, boost::mpl::vector3, std::allocator > const&, RDKit::Trajectory&> > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 5# 0x00007F488FE1B62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x00007F891D7B462C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 11# 0x00007F488D9B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 12# 0x00007F488D9B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 13# 0x00007F488D9B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 14# 0x00007F488D9B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 15# 0x00007F488D9B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 11# 0x00007F891B3B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 12# 0x00007F891B3B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 13# 0x00007F891B3B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 14# 0x00007F891B3B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 15# 0x00007F891B3B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 21# 0x00007F488FE183C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 21# 0x00007F891D7B13C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 22# _PyObject_MakeTpCall in /usr/bin/python3 197: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 24# 0x00000000005CD3C9 in /usr/bin/python3 @@ -30478,13 +30286,13 @@ 197: 50# 0x00000000006B921E in /usr/bin/python3 197: 51# Py_RunMain in /usr/bin/python3 197: 52# Py_BytesMain in /usr/bin/python3 -197: 53# 0x00007F48905C4CA8 in /lib/x86_64-linux-gnu/libc.so.6 +197: 53# 0x00007F891DF5DCA8 in /lib/x86_64-linux-gnu/libc.so.6 197: 54# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 197: 55# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: ..[17:55:23] +197: ..[14:17:47] 197: 197: **** 197: Pre-condition Violation @@ -30498,23 +30306,23 @@ 197: 2# RDKit::readGromosTrajectory(std::__cxx11::basic_string, std::allocator > const&, RDKit::Trajectory&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 197: 3# boost::python::objects::caller_py_function_impl, std::allocator > const&, RDKit::Trajectory&), boost::python::default_call_policies, boost::mpl::vector3, std::allocator > const&, RDKit::Trajectory&> > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 5# 0x00007F488FE1B62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x00007F891D7B462C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 11# 0x00007F488D9B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 12# 0x00007F488D9B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 13# 0x00007F488D9B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 14# 0x00007F488D9B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 15# 0x00007F488D9B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 11# 0x00007F891B3B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 12# 0x00007F891B3B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 13# 0x00007F891B3B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 14# 0x00007F891B3B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 15# 0x00007F891B3B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 21# 0x00007F488FE183C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 21# 0x00007F891D7B13C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 22# _PyObject_MakeTpCall in /usr/bin/python3 197: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 24# 0x00000000005CD3C9 in /usr/bin/python3 @@ -30546,15 +30354,18 @@ 197: 50# 0x00000000006B921E in /usr/bin/python3 197: 51# Py_RunMain in /usr/bin/python3 197: 52# Py_BytesMain in /usr/bin/python3 -197: 53# 0x00007F48905C4CA8 in /lib/x86_64-linux-gnu/libc.so.6 +197: 53# 0x00007F891DF5DCA8 in /lib/x86_64-linux-gnu/libc.so.6 197: 54# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 197: 55# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: .[17:55:23] +197: .[14:17:47] 197: 197: **** +160: file testGithub4764.sz1.svg gave hash 2364628953U not the expected 3611125861U +160: file testGithub4764.sz2.svg gave hash 1490175526U not the expected 1936114454U +160: file testGithub4764.sz3.svg gave hash 1662881340U not the expected 2712214121U 197: Pre-condition Violation 197: d_pos must not be NULL 197: Violation occurred on line 23 in file ./Code/GraphMol/Trajectory/Trajectory.cpp @@ -30566,23 +30377,23 @@ 197: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 197: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 5# 0x00007F488FE1B62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x00007F891D7B462C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 11# 0x00007F488D9B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 12# 0x00007F488D9B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 13# 0x00007F488D9B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 14# 0x00007F488D9B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 15# 0x00007F488D9B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 11# 0x00007F891B3B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 12# 0x00007F891B3B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 13# 0x00007F891B3B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 14# 0x00007F891B3B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 15# 0x00007F891B3B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 21# 0x00007F488FE183C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 21# 0x00007F891D7B13C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 22# _PyObject_MakeTpCall in /usr/bin/python3 197: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 24# 0x00000000005CD3C9 in /usr/bin/python3 @@ -30614,13 +30425,13 @@ 197: 50# 0x00000000006B921E in /usr/bin/python3 197: 51# Py_RunMain in /usr/bin/python3 197: 52# Py_BytesMain in /usr/bin/python3 -197: 53# 0x00007F48905C4CA8 in /lib/x86_64-linux-gnu/libc.so.6 +197: 53# 0x00007F891DF5DCA8 in /lib/x86_64-linux-gnu/libc.so.6 197: 54# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 197: 55# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: [17:55:23] +197: [14:17:47] 197: 197: **** 197: Pre-condition Violation @@ -30634,23 +30445,23 @@ 197: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 197: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 5# 0x00007F488FE1B62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x00007F891D7B462C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 11# 0x00007F488D9B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 12# 0x00007F488D9B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 13# 0x00007F488D9B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 14# 0x00007F488D9B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 15# 0x00007F488D9B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 11# 0x00007F891B3B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 12# 0x00007F891B3B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 13# 0x00007F891B3B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 14# 0x00007F891B3B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 15# 0x00007F891B3B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 21# 0x00007F488FE183C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 21# 0x00007F891D7B13C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 22# _PyObject_MakeTpCall in /usr/bin/python3 197: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 24# 0x00000000005CD3C9 in /usr/bin/python3 @@ -30682,13 +30493,13 @@ 197: 50# 0x00000000006B921E in /usr/bin/python3 197: 51# Py_RunMain in /usr/bin/python3 197: 52# Py_BytesMain in /usr/bin/python3 -197: 53# 0x00007F48905C4CA8 in /lib/x86_64-linux-gnu/libc.so.6 +197: 53# 0x00007F891DF5DCA8 in /lib/x86_64-linux-gnu/libc.so.6 197: 54# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 197: 55# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: .[17:55:23] +197: .[14:17:47] 197: 197: **** 197: Range Error @@ -30703,23 +30514,23 @@ 197: 3# RDKit::getSnapshot_wrap(RDKit::Trajectory*, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 4# boost::python::objects::caller_py_function_impl, boost::mpl::vector3 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 6# 0x00007F488FE1B62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 6# 0x00007F891D7B462C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 12# 0x00007F488D9B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 13# 0x00007F488D9B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 14# 0x00007F488D9B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 15# 0x00007F488D9B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 16# 0x00007F488D9B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 12# 0x00007F891B3B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 13# 0x00007F891B3B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 14# 0x00007F891B3B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 15# 0x00007F891B3B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 16# 0x00007F891B3B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 20# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 21# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 22# 0x00007F488FE183C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 22# 0x00007F891D7B13C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 23# _PyObject_MakeTpCall in /usr/bin/python3 197: 24# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 25# 0x00000000005CD3C9 in /usr/bin/python3 @@ -30751,26 +30562,15 @@ 197: 51# 0x00000000006B921E in /usr/bin/python3 197: 52# Py_RunMain in /usr/bin/python3 197: 53# Py_BytesMain in /usr/bin/python3 -197: 54# 0x00007F48905C4CA8 in /lib/x86_64-linux-gnu/libc.so.6 +197: 54# 0x00007F891DF5DCA8 in /lib/x86_64-linux-gnu/libc.so.6 197: 55# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 197: 56# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: [17:55:23] +197: [14:17:47] 197: 197: **** -143: [17:55:23] diphenylmethylidencyclobutane 79.6139 -143: [17:55:23] done -143: [17:55:23] ------------------------------------- -143: [17:55:23] Test Github Issue 613: UFF Atom type not properly assigned to lanthanides. -143: [17:55:23] done -143: [17:55:23] ------------------------------------- -143: [17:55:23] Test square planar complexes -143: [17:55:23] done -143: [17:55:23] ------------------------------------- -143: [17:55:23] Test octahedral complexes -143: [17:55:23] done 197: Range Error 197: pointNum 197: Violation occurred on line 27 in file ./Code/GraphMol/Trajectory/Trajectory.cpp @@ -30782,23 +30582,23 @@ 197: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 197: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 5# 0x00007F488FE1B62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x00007F891D7B462C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 11# 0x00007F488D9B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 12# 0x00007F488D9B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 13# 0x00007F488D9B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 14# 0x00007F488D9B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 15# 0x00007F488D9B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 11# 0x00007F891B3B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 12# 0x00007F891B3B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 13# 0x00007F891B3B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 14# 0x00007F891B3B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 15# 0x00007F891B3B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 21# 0x00007F488FE183C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 21# 0x00007F891D7B13C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 22# _PyObject_MakeTpCall in /usr/bin/python3 197: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 24# 0x00000000005CD3C9 in /usr/bin/python3 @@ -30830,13 +30630,13 @@ 197: 50# 0x00000000006B921E in /usr/bin/python3 197: 51# Py_RunMain in /usr/bin/python3 197: 52# Py_BytesMain in /usr/bin/python3 -197: 53# 0x00007F48905C4CA8 in /lib/x86_64-linux-gnu/libc.so.6 +197: 53# 0x00007F891DF5DCA8 in /lib/x86_64-linux-gnu/libc.so.6 197: 54# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 197: 55# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: .[17:55:23] +197: .[14:17:47] 197: 197: **** 197: Range Error @@ -30851,23 +30651,23 @@ 197: 3# RDKit::getSnapshot_wrap(RDKit::Trajectory*, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 4# boost::python::objects::caller_py_function_impl, boost::mpl::vector3 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 6# 0x00007F488FE1B62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 6# 0x00007F891D7B462C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 12# 0x00007F488D9B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 13# 0x00007F488D9B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 14# 0x00007F488D9B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 15# 0x00007F488D9B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 16# 0x00007F488D9B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 12# 0x00007F891B3B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 13# 0x00007F891B3B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 14# 0x00007F891B3B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 15# 0x00007F891B3B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 16# 0x00007F891B3B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 20# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 21# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 22# 0x00007F488FE183C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 22# 0x00007F891D7B13C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 23# _PyObject_MakeTpCall in /usr/bin/python3 197: 24# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 25# 0x00000000005CD3C9 in /usr/bin/python3 @@ -30899,13 +30699,81 @@ 197: 51# 0x00000000006B921E in /usr/bin/python3 197: 52# Py_RunMain in /usr/bin/python3 197: 53# Py_BytesMain in /usr/bin/python3 -197: 54# 0x00007F48905C4CA8 in /lib/x86_64-linux-gnu/libc.so.6 +197: 54# 0x00007F891DF5DCA8 in /lib/x86_64-linux-gnu/libc.so.6 197: 55# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 197: 56# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: [17:55:23] +197: [14:17:47] +197: +197: **** +197: Pre-condition Violation +197: d_dimension must be == 2 +197: Violation occurred on line 25 in file ./Code/GraphMol/Trajectory/Trajectory.cpp +197: Failed Expression: d_trajectory->dimension() == 2 +197: ---------- +197: Stacktrace: +197: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +197: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +197: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 +197: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so +197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x00007F891D7B462C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so +197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so +197: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so +197: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 11# 0x00007F891B3B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 12# 0x00007F891B3B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 13# 0x00007F891B3B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 14# 0x00007F891B3B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 15# 0x00007F891B3B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so +197: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so +197: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so +197: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so +197: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 21# 0x00007F891D7B13C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 22# _PyObject_MakeTpCall in /usr/bin/python3 +197: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 +197: 24# 0x00000000005CD3C9 in /usr/bin/python3 +197: 25# _PyEval_EvalFrameDefault in /usr/bin/python3 +197: 26# 0x0000000000690C6F in /usr/bin/python3 +197: 27# 0x000000000062D590 in /usr/bin/python3 +197: 28# _PyObject_MakeTpCall in /usr/bin/python3 +197: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 +197: 30# 0x00000000005CD3C9 in /usr/bin/python3 +197: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 +197: 32# 0x0000000000690C6F in /usr/bin/python3 +197: 33# 0x000000000062D590 in /usr/bin/python3 +197: 34# _PyObject_MakeTpCall in /usr/bin/python3 +197: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 +197: 36# 0x00000000005CD3C9 in /usr/bin/python3 +197: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 +197: 38# 0x0000000000690C6F in /usr/bin/python3 +197: 39# 0x000000000062D590 in /usr/bin/python3 +197: 40# _PyObject_MakeTpCall in /usr/bin/python3 +197: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 +197: 42# 0x00000000005A090C in /usr/bin/python3 +197: 43# _PyObject_MakeTpCall in /usr/bin/python3 +197: 44# _PyEval_EvalFrameDefault in /usr/bin/python3 +197: 45# PyEval_EvalCode in /usr/bin/python3 +197: 46# 0x00000000006AB8D1 in /usr/bin/python3 +197: 47# 0x00000000006A899C in /usr/bin/python3 +197: 48# 0x00000000006B9943 in /usr/bin/python3 +197: 49# 0x00000000006B93E3 in /usr/bin/python3 +197: 50# 0x00000000006B921E in /usr/bin/python3 +197: 51# Py_RunMain in /usr/bin/python3 +197: 52# Py_BytesMain in /usr/bin/python3 +197: 53# 0x00007F891DF5DCA8 in /lib/x86_64-linux-gnu/libc.so.6 +197: 54# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +197: 55# _start in /usr/bin/python3 +197: ---------- +197: **** +197: +197: [14:17:47] 197: 197: **** 197: Pre-condition Violation @@ -30919,23 +30787,23 @@ 197: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 197: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 5# 0x00007F488FE1B62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x00007F891D7B462C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 11# 0x00007F488D9B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 12# 0x00007F488D9B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 13# 0x00007F488D9B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 14# 0x00007F488D9B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 15# 0x00007F488D9B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 11# 0x00007F891B3B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 12# 0x00007F891B3B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 13# 0x00007F891B3B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 14# 0x00007F891B3B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 15# 0x00007F891B3B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 21# 0x00007F488FE183C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 21# 0x00007F891D7B13C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 22# _PyObject_MakeTpCall in /usr/bin/python3 197: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 24# 0x00000000005CD3C9 in /usr/bin/python3 @@ -30967,113 +30835,644 @@ 197: 50# 0x00000000006B921E in /usr/bin/python3 197: 51# Py_RunMain in /usr/bin/python3 197: 52# Py_BytesMain in /usr/bin/python3 -197: 53# 0x00007F48905C4CA8 in /lib/x86_64-linux-gnu/libc.so.6 +197: 53# 0x00007F891DF5DCA8 in /lib/x86_64-linux-gnu/libc.so.6 197: 54# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 197: 55# _start in /usr/bin/python3 197: ---------- 197: **** 197: -40: [17:55:23] Finished -40: [17:55:23] testing github #1567: Non-canonical result from MolFragmentToSmiles() -40: [17:55:23] Finished -161/236 Test #143: testUFFForceFieldHelpers ............... Passed 3.59 sec +197: . +197: ---------------------------------------------------------------------- +197: Ran 9 tests in 0.366s +197: +197: OK +197: Testing Trajectory wrapper +160: file testGithub4764.sz1.png gave hash 517897906U not the expected 2179222277U +162/236 Test #198: pyTestSGroups .......................... Passed 0.63 sec +test 202 + Start 202: pyCDXMLTest + +202: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/test_cdxml.py" +202: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap +202: Test timeout computed to be: 1500 +151: 1457316616 +151: =============================================================================== +151: All tests passed (73 assertions in 3 test cases) +151: +160: file testGithub4764.sz2.png gave hash 2568067924U not the expected 444262090U +163/236 Test #151: molAlignCatchTest ...................... Passed 7.02 sec +164/236 Test #197: pyTestTrajectory ....................... Passed 0.68 sec test 203 Start 203: molStandardizeTest 203: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeTest 203: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize 203: Test timeout computed to be: 1500 -162/236 Test #40: hanoiTest .............................. Passed 6.83 sec test 204 Start 204: molNormalizeTest -204: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molNormalizeTest -204: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize -204: Test timeout computed to be: 1500 -197: [17:55:23] -197: -197: **** -197: Pre-condition Violation -197: d_dimension must be == 2 -197: Violation occurred on line 25 in file ./Code/GraphMol/Trajectory/Trajectory.cpp -197: Failed Expression: d_trajectory->dimension() == 2 -197: ---------- -197: Stacktrace: -197: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -197: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -197: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 -197: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so -197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 5# 0x00007F488FE1B62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so -197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so -197: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so -197: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 11# 0x00007F488D9B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 12# 0x00007F488D9B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 13# 0x00007F488D9B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 14# 0x00007F488D9B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 15# 0x00007F488D9B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so -197: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so -197: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so -197: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so -197: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 21# 0x00007F488FE183C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 22# _PyObject_MakeTpCall in /usr/bin/python3 -197: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 -197: 24# 0x00000000005CD3C9 in /usr/bin/python3 -197: 25# _PyEval_EvalFrameDefault in /usr/bin/python3 -197: 26# 0x0000000000690C6F in /usr/bin/python3 -197: 27# 0x000000000062D590 in /usr/bin/python3 -197: 28# _PyObject_MakeTpCall in /usr/bin/python3 -197: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 -197: 30# 0x00000000005CD3C9 in /usr/bin/python3 -197: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 -197: 32# 0x0000000000690C6F in /usr/bin/python3 -197: 33# 0x000000000062D590 in /usr/bin/python3 -197: 34# _PyObject_MakeTpCall in /usr/bin/python3 -197: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 -197: 36# 0x00000000005CD3C9 in /usr/bin/python3 -197: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 -197: 38# 0x0000000000690C6F in /usr/bin/python3 -197: 39# 0x000000000062D590 in /usr/bin/python3 -197: 40# _PyObject_MakeTpCall in /usr/bin/python3 -197: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 -197: 42# 0x00000000005A090C in /usr/bin/python3 -197: 43# _PyObject_MakeTpCall in /usr/bin/python3 -197: 44# _PyEval_EvalFrameDefault in /usr/bin/python3 -197: 45# PyEval_EvalCode in /usr/bin/python3 -197: 46# 0x00000000006AB8D1 in /usr/bin/python3 -197: 47# 0x00000000006A899C in /usr/bin/python3 -197: 48# 0x00000000006B9943 in /usr/bin/python3 -197: 49# 0x00000000006B93E3 in /usr/bin/python3 -197: 50# 0x00000000006B921E in /usr/bin/python3 -197: 51# Py_RunMain in /usr/bin/python3 -197: 52# Py_BytesMain in /usr/bin/python3 -197: 53# 0x00007F48905C4CA8 in /lib/x86_64-linux-gnu/libc.so.6 -197: 54# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -197: 55# _start in /usr/bin/python3 -197: ---------- -197: **** -197: -197: . -197: ---------------------------------------------------------------------- -197: Ran 9 tests in 0.459s -197: -197: OK -197: Testing Trajectory wrapper -163/236 Test #196: pyTestConformerWrap .................... Passed 1.06 sec -test 205 - Start 205: molValidateTest +204: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molNormalizeTest +204: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize +204: Test timeout computed to be: 1500 +160: file testGithub4764.sz3.png gave hash 2910755141U not the expected 3567162200U +160: file github5383_1.svg gave hash 4241964660U not the expected 1815941817U +160: file github5383_2.svg gave hash 2560846108U not the expected 0U +160: file github5383_1.png gave hash 1118153320U not the expected 2893520928U +160: file acs1996_1.png gave hash 1014030062U not the expected 2329725800U +160: file acs1996_2.png gave hash 1604110899U not the expected 2996350718U +160: file acs1996_3.svg gave hash 3058522544U not the expected 879041204U +204: [14:17:47] Can't kekulize mol. Unkekulized atoms: 3 7 8 9 +160: [14:17:47] ACS drawing mode works best with a flexiCanvas i.e. a drawer created with width and height of -1. The scale will be fixed, and that may not look great with a pre-determined size. +160: file bond_highlights_8.svg gave hash 3610726614U not the expected 3119784980U +69: [14:17:48] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +69: [14:17:48] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +160: file test_github6112.svg gave hash 3865338574U not the expected 3278777629U +163: MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds +163: Time elapsed 0.000 seconds +163: +163: test32() +163: 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 +163: Time elapsed 0.149 seconds +163: +163: test190() +163: 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 +163: Time elapsed 0.022 seconds +163: +163: test3() +163: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6]-[#6](=[#8])-[#7]-[#6]-[#6]-[#6]-[#6] 14 atoms, 14 bonds +163: Time elapsed 0.025 seconds +163: +163: testSimpleFast() +163: 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 +163: Time elapsed 0.164 seconds +163: +163: testSimple() +163: MCS: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds +163: Time elapsed 0.100 seconds +163: MCS MatchFusedRings: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds +163: Time elapsed 0.140 seconds +163: MCS MatchFusedRingsStrict: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds +163: Time elapsed 0.213 seconds +163: +163: testSegFault() +163: MCS: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds +163: Time elapsed 0.038 seconds +163: MCS MatchFusedRings: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds +163: Time elapsed 0.030 seconds +163: 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 +163: Time elapsed 0.057 seconds +163: +163: testThreshold() +163: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds +163: Time elapsed 0.012 seconds +163: +163: testRing1() +163: 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 +163: Time elapsed 1.441 seconds +163: 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 +163: Time elapsed 1.950 seconds +163: 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 +163: Time elapsed 2.191 seconds +163: +163: testAtomCompareIsotopes() +163: MCS: [0*]-[0*]-[13*] 3 atoms, 2 bonds +163: Time elapsed 0.000 seconds +163: +163: testAtomCompareAnyAtom() +163: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#7,#8,#9,#17] 7 atoms, 7 bonds +163: Time elapsed 0.000 seconds +163: +163: testAtomCompareAnyAtom() +163: MCS: [#6]1-,:[#6]-,:[#6]-,:[#6]-,:[#6]-,:[#6]-,:1=,-[#6,#7,#8,#9,#17] 7 atoms, 7 bonds +163: Time elapsed 0.000 seconds +163: +163: testAtomCompareAnyAtom() +163: MCS: [#1]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#8] 8 atoms, 8 bonds +163: Time elapsed 0.000 seconds +163: +163: testAtomCompareAnyAtom() +163: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#8] 7 atoms, 7 bonds +163: Time elapsed 0.000 seconds +163: +163: testJnk1LigandsDistance() +163: 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 +40: [14:17:48] Finished +40: [14:17:48] testing github #1567: Non-canonical result from MolFragmentToSmiles() +163: Time elapsed 0.019 seconds +163: 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 +40: [14:17:48] Finished +165/236 Test #40: hanoiTest .............................. Passed 11.14 sec +test 205 + Start 205: molValidateTest + +205: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molValidateTest +205: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize +205: Test timeout computed to be: 1500 +29: +29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.sdf... +111: [14:17:48] done +111: [14:17:48] ------------------------------------- +111: [14:17:48] Test Issue252: Bad definitions for Crippen atom types. +111: [14:17:48] done +111: [14:17:48] ------------------------------------- +111: [14:17:48] Test calculation of ChiVs. +111: [14:17:48] done +111: [14:17:48] ------------------------------------- +111: [14:17:48] Test calculation of ChiNs. +186: iterative +205: ERROR: [FeaturesValidation] Query atom 0 is not allowed +205: ERROR: [FeaturesValidation] Dummy atom 0 is not allowed +205: ERROR: [FeaturesValidation] Query bond 0 is not allowed +205: ERROR: [FeaturesValidation] Bond 0 of aromatic type is not allowed +205: ERROR: [FeaturesValidation] Bond 1 of aromatic type is not allowed +205: ERROR: [FeaturesValidation] Bond 2 of aromatic type is not allowed +205: ERROR: [FeaturesValidation] Bond 3 of aromatic type is not allowed +205: ERROR: [FeaturesValidation] Bond 5 of aromatic type is not allowed +205: ERROR: [FeaturesValidation] Bond 6 of aromatic type is not allowed +205: ERROR: [FeaturesValidation] Bond 2 of dative type is not allowed +205: ERROR: [FeaturesValidation] Bond 3 of dative type is not allowed +205: ERROR: [FeaturesValidation] Atom 2 with alias 'CF3' is not allowed +205: ERROR: [FeaturesValidation] Enhanced stereochemistry features are not allowed +205: ERROR: [StereoValidation] Atom 3 has both unknown and wedged/dashed stereo bonds. +205: here +205: ERROR: [StereoValidation] Bond 3 has assigned stereo type, but unexpected bond order. +205: there +205: ERROR: [StereoValidation] Atom 0 has stereo bonds, but less than 3 explicit substituents. +166/236 Test #205: molValidateTest ........................ Passed 0.08 sec +test 206 + Start 206: molChargeTest + +206: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molChargeTest +206: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize +206: Test timeout computed to be: 1500 +111: [14:17:48] done +111: [14:17:48] ------------------------------------- +111: [14:17:48] Test calculation of HallKierAlpha. +111: [14:17:48] done +111: [14:17:48] ------------------------------------- +111: [14:17:48] Test calculation of Kappa1. +111: [14:17:48] done +111: [14:17:48] ------------------------------------- +111: [14:17:48] Test calculation of Kappa2. +202: . +202: ---------------------------------------------------------------------- +202: Ran 1 test in 0.013s +202: +202: OK +111: [14:17:48] done +111: [14:17:48] ------------------------------------- +111: [14:17:48] Test calculation of Kappa3. +111: [14:17:48] done +111: [14:17:48] ------------------------------------- +111: [14:17:48] Test Crippen atom type calculations. +111: [14:17:48] done +111: [14:17:48] ------------------------------------- +111: [14:17:48] Test ring descriptors +111: [14:17:48] done +111: [14:17:48] ------------------------------------- +111: [14:17:48] Test other count descriptors. +111: [14:17:48] done +111: [14:17:48] ------------------------------------- +111: [14:17:48] Test MQN +143: [14:17:48] done +143: [14:17:48] ------------------------------------- +143: [14:17:48] Test UFF multithreading3 +69: ---------------------------------- +69: ---------------------------------- +204: [14:17:48] Initializing Normalizer +204: [14:17:48] Running Normalizer +204: [14:17:48] Rule applied: BrokenazidetoN=N+=N- +204: [14:17:48] Initializing Normalizer +204: [14:17:48] Running Normalizer +204: [14:17:48] Initializing Normalizer +204: [14:17:48] Running Normalizer +69: [14:17:48] +69: +69: **** +69: Pre-condition Violation +69: rlabel out of range for MDL files +69: Violation occurred on line 863 in file ./Code/GraphMol/Atom.cpp +69: Failed Expression: rlabel >= 0 && rlabel < 100 +69: ---------- +69: Stacktrace: +69: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +69: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +69: 2# RDKit::setAtomRLabel(RDKit::Atom*, int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +69: 3# 0x000055AD5A89EFFF in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 4# 0x000055AD5A8F83EA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 5# 0x000055AD5A8789A3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 6# 0x00007FECAE833CA8 in /lib/x86_64-linux-gnu/libc.so.6 +69: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +69: 8# 0x000055AD5A878AD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: ---------- +69: **** +69: +69: [14:17:48] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +201: [14:17:48] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. +201: [14:17:48] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. +201: [14:17:48] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. +111: [14:17:48] done +111: [14:17:48] ------------------------------------- +111: [14:17:48] Test GitHub Issue 56. +111: [14:17:48] WARNING: not removing hydrogen atom without neighbors +111: [14:17:48] WARNING: not removing hydrogen atom without neighbors +111: [14:17:48] WARNING: not removing hydrogen atom without neighbors +111: [14:17:48] WARNING: not removing hydrogen atom without neighbors +111: [14:17:48] done +111: [14:17:48] ------------------------------------- +111: [14:17:48] Test Github92: Bad Crippen atom type for pyrrole H. +111: [14:17:48] done +111: [14:17:48] ------------------------------------- +111: [14:17:48] Test Github362: order dependence in Kier-Hall descriptors. +111: [14:17:48] done +111: [14:17:48] ------------------------------------- +111: [14:17:48] Test calculation of spiro and bridgehead counts. +111: [14:17:48] done +111: [14:17:48] ------------------------------------- +111: [14:17:48] Test Github694: ExactMolWt ignoring the mass of the electron +111: [14:17:48] done +111: [14:17:48] ------------------------------------- +111: [14:17:48] Testing Properties and KitchenSink +201: .[14:17:48] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. +201: [14:17:48] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. +201: [14:17:48] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. +201: ...[14:17:48] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. +201: [14:17:48] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. +201: [14:17:48] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. +201: . +201: ---------------------------------------------------------------------- +167/236 Test #204: molNormalizeTest ....................... Passed 0.57 sec +test 207 + Start 207: molTautomerTest + +207: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molTautomerTest +207: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize +207: Test timeout computed to be: 1500 +111: [14:17:48] ---Caught keyerror (bad property name)--- +111: [14:17:48] ------------------------------------- +111: [14:17:48] Test USR Descriptor +201: Ran 5 tests in 0.042s +201: +201: OK +111: [14:17:48] done +111: [14:17:48] ------------------------------------- +111: [14:17:48] Test Github #1702: AUTOCORR2D.h not installed unless RDK_BUILD_DESCRIPTORS3D but is required +111: [14:17:48] done +111: [14:17:48] ------------------------------------- +111: [14:17:48] Test Github #1973: support P and S terms for TPSA calculation +111: [14:17:48] done +111: [14:17:48] ------------------------------------- +111: [14:17:48] Test Github #2948: Empty molecule has non-zero LabuteASA +111: [14:17:48] done +168/236 Test #111: testDescriptors ........................ Passed 9.87 sec +test 208 + Start 208: molStandardizeSmallTest + +208: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeSmallTest +208: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize +208: Test timeout computed to be: 1500 +169/236 Test #202: pyCDXMLTest ............................ Passed 0.67 sec +170/236 Test #206: molChargeTest .......................... Passed 0.13 sec +test 209 + Start 209: molFragmentTest + +209: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molFragmentTest +209: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize +209: Test timeout computed to be: 1500 +test 210 + Start 210: molStandardizeCatchTest + +210: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeCatchTest +210: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize +210: Test timeout computed to be: 1500 +150: *********************************************************** +150: Testing O3AAlign +150: --------------------------------- +150: testMMFFO3A +150: +150: --------------------------------- +150: testMMFFO3A with pre-computed dmat and MolHistogram +150: +150: --------------------------------- +150: testMMFFO3A with constraints +150: +150: --------------------------------- +150: testMMFFO3A with variable weight constraints followed by local-only optimization +150: +150: --------------------------------- +150: testCrippenO3A +150: +150: --------------------------------- +150: testCrippenO3A with pre-computed dmat and MolHistogram +150: +150: --------------------------------- +150: testCrippenO3A with constraints +150: +150: --------------------------------- +150: testCrippenO3A with variable weight constraints followed by local-only optimization +150: +150: --------------------------------- +150: testMMFFO3A multithreading +150: +150: generating reference data +171/236 Test #208: molStandardizeSmallTest ................ Passed 0.08 sec +test 211 + Start 211: molStandardizePipelineTest + +211: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizePipelineTest +211: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize +211: Test timeout computed to be: 1500 +172/236 Test #201: pyTestPropertyLists .................... Passed 0.91 sec +test 212 + Start 212: pyMolStandardize + +212: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Wrap/testMolStandardize.py" +212: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap +212: Test timeout computed to be: 1500 +160: file AtropManyChiralsEnhanced.svg gave hash 3443464321U not the expected 2256768013U +209: [14:17:48] SMARTS Parse Error: syntax error while parsing: [Cl +209: [14:17:48] SMARTS Parse Error: Failed parsing SMARTS '[Cl' for input: '[Cl' +173/236 Test #209: molFragmentTest ........................ Passed 0.15 sec +test 213 + Start 213: testScaffoldNetwork + +213: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/testScaffoldNetwork +213: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork +213: Test timeout computed to be: 1500 +211: Randomness seeded to: 673258900 +211: 1 Counts line too short: '' on line4 +211: 1 Could not instantiate a valid molecule from input +211: 8 Molecule has no atoms +211: [14:17:48] Explicit valence for atom # 1 N, 4, is greater than permitted +211: [14:17:48] Explicit valence for atom # 1 N, 4, is greater than permitted +211: 8 Explicit valence for atom # 1 N, 4, is greater than permitted +211: 128 An error occurred while preparing the molecule for standardization. +211: 8 The molecule contains an unknown isotope: 3C +211: 4 Query atom 0 is not allowed +195: ..............[14:17:48] SMARTS Parse Error: syntax error while parsing: fiib +195: [14:17:48] SMARTS Parse Error: Failed parsing SMARTS 'fiib' for input: 'fiib' +211: 4 Bond 0 of aromatic type is not allowed +211: 4 Bond 1 of aromatic type is not allowed +211: 4 Bond 2 of aromatic type is not allowed +211: 4 Bond 3 of aromatic type is not allowed +211: 4 Bond 5 of aromatic type is not allowed +211: 4 Bond 6 of aromatic type is not allowed +211: 4 Bond 2 of dative type is not allowed +211: 4 Bond 3 of dative type is not allowed +211: 4 Enhanced stereochemistry features are not allowed +211: 8 The radical at atom 0 is not allowed +211: [14:17:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +211: 16 The molecule includes non-null Z coordinates +160: file testGithub_7739_1.svg gave hash 3358510977U not the expected 2615562225U +210: Randomness seeded to: 2310413425 +210: * - * - * - * m1 +211: 32 Atom 0 too close to bond 2 +210: * - * - * - * m2 +210: * - * - * - * m1 +210: * - * - * - * m2 +210: [14:17:48] Can't kekulize mol. Unkekulized atoms: 3 7 +211: 32 The length of bond 3 between atoms 0 and 3 exceeds a configured limit +210: [14:17:48] Can't kekulize mol. Unkekulized atoms: 3 8 +195: ....[14:17:48] ERROR: Problems encountered parsing data fields +195: [14:17:48] ERROR: moving to the beginning of the next molecule +195: [14:17:48] ERROR: Problems encountered parsing data fields +195: [14:17:48] ERROR: moving to the beginning of the next molecule +195: [14:17:48] Spurious data before the first property will be ignored +195: [14:17:48] Property will be truncated after the first blank line +195: [14:17:48] Property will be truncated after the first blank line +195: [14:17:48] Property will be truncated after the first blank line +195: [14:17:48] ERROR: Problems encountered parsing data fields +195: [14:17:48] ERROR: moving to the beginning of the next molecule +195: [14:17:48] ERROR: Problems encountered parsing data fields +195: [14:17:48] ERROR: moving to the beginning of the next molecule +195: [14:17:48] Spurious data before the first property will be ignored +195: [14:17:48] Property will be truncated after the first blank line +195: [14:17:48] Property will be truncated after the first blank line +195: [14:17:48] Property will be truncated after the first blank line +195: [14:17:48] ERROR: Problems encountered parsing data fields +195: [14:17:48] ERROR: moving to the beginning of the next molecule +195: [14:17:48] Property will be truncated after the first blank line +195: [14:17:48] ERROR: Problems encountered parsing data fields +195: [14:17:48] ERROR: moving to the beginning of the next molecule +195: [14:17:48] Property will be truncated after the first blank line +210: [14:17:48] Can't kekulize mol. Unkekulized atoms: 2 3 4 +195: .[14:17:48] SMILES Parse Error: syntax error while parsing: fail +195: [14:17:48] SMILES Parse Error: check for mistakes around position 1: +195: [14:17:48] fail +195: [14:17:48] ^ +195: [14:17:48] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' +195: [14:17:48] ERROR: Smiles parse error on line 2 +195: [14:17:48] ERROR: Cannot create molecule from : 'fail' +160: file testGithub_7739_3.svg gave hash 176211825U not the expected 1037942338U +195: >>> This may result in an infinite loop. It should finish almost instantly +195: <<< OK, it finished. +211: 64 Atom 0 has 3 explicit substituents and multiple stereo bonds +163: Time elapsed 0.022 seconds +163: +163: test18() +163: 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 +163: 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 +163: Time elapsed 0.019 seconds +163: +163: test504() +163: 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 +163: 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 +163: Time elapsed 0.493 seconds +163: MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds +163: Time elapsed 0.013 seconds +163: 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 +163: Time elapsed 0.162 seconds +163: Query Cc1c(F)c(N2CCNC(C)C2)cc2c1c(=O)c(C(=O)O)cn2C1CC1 26(26) atoms, 29(28) bonds +163: 1 Seeds:1 MCS 25 atoms, 28 bonds for 0.0408 seconds. bond[0]=6 +163: STATISTICS: +163: Total Growing Steps = 1, MCS found on 1 step, for 0.0408 seconds +163: Initial Seeds = 1, Mismatched 0 +163: Inspected Seeds = 2 +163: Rejected by BestSize = 0 +163: IndividualBondExcluded = 0 +163: MatchCheck Seeds = 2 +163: MatchCalls = 2 +163: MatchFound = 1 +163: fastMatchCalls = 1 +163: fastMatchFound = 0 +163: slowMatchCalls = 2 +163: slowMatchFound = 1 +163: DupCacheFound = 0 0 matched, 0 mismatched +163: HashCache size = 1 keys +163: HashCache size = 1 entries +163: FindHashInCache = 2 +163: HashFoundInCache= 0 +163: ExactMatchCalls = 0 +163: ExactMatchFound = 0 +163: Time elapsed 0.041 seconds +163: query=OCCl SubstructMatch(useChirality=false) res =1 size=3 +163: query=OCCl SubstructMatch(useChirality=true ) res =1 size=3 +163: test target = O[C@H](F)CCl query = C(F)C useChirality = 0 +163: res sub = 1 size=3 +163: MCS: [#6](-[#9])-[#6] 3 atoms, 2 bonds +163: test target = O[C@H](F)CCl query = C(F)C useChirality = 1 +163: res sub = 1 size=3 +163: MCS: [#6](-[#9])-[#6] 3 atoms, 2 bonds +163: test target = CC[C@H](F)Cl query = CCC useChirality = 0 +163: res sub = 1 size=3 +163: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds +163: test target = CC[C@H](F)Cl query = CCC useChirality = 1 +163: res sub = 1 size=3 +163: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds +163: test target = CCC(F)Cl query = CC useChirality = 0 +163: res sub = 1 size=2 +163: MCS: [#6]-[#6] 2 atoms, 1 bonds +163: test target = CCC(F)Cl query = CC useChirality = 1 +163: res sub = 1 size=2 +163: MCS: [#6]-[#6] 2 atoms, 1 bonds +163: test target = C[C@H](F)CCl query = C[C@H](F)C useChirality = 0 +163: res sub = 1 size=4 +163: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +163: test target = C[C@H](F)CCl query = C[C@H](F)C useChirality = 1 +163: res sub = 1 size=4 +163: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +163: test target = C[C@H](F)CCl query = C[C@@H](F)C useChirality = 0 +163: res sub = 1 size=4 +163: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +163: test target = C[C@H](F)CCl query = C[C@@H](F)C useChirality = 1 +163: res sub = 1 size=4 +163: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +163: test target = O[C@H](F)CCl query = CC(F)C useChirality = 0 +163: res sub = 0 size=0 +163: MCS: [#6]-[#6]-[#9] 3 atoms, 2 bonds +163: test target = O[C@H](F)CCl query = CC(F)C useChirality = 1 +163: res sub = 0 size=0 +163: MCS: [#6]-[#6]-[#9] 3 atoms, 2 bonds +163: test target = O[C@H](F)CCl query = OC(F)C useChirality = 0 +163: res sub = 1 size=4 +163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +163: test target = O[C@H](F)CCl query = OC(F)C useChirality = 1 +211: 64 Atom 0 has adjacent stereo bonds with like orientation +211: [14:17:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +160: file testGithub_7739_4.svg gave hash 3309264286U not the expected 3549083171U +211: 16 The molecule includes non-null Z coordinates +211: 64 Atom 0 has adjacent stereo bonds with like orientation +160: file testSmallReactionCanvas.svg gave hash 3859901121U not the expected 2238356155U +163: res sub = 1 size=4 +163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +163: test target = O[C@H](F)CCl query = O[C@H](F)C useChirality = 0 +163: res sub = 1 size=4 +163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +163: test target = O[C@H](F)CCl query = O[C@H](F)C useChirality = 1 +163: res sub = 1 size=4 +163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +163: test target = O[C@H](F)CCl query = O[C@@H](F)C useChirality = 0 +163: res sub = 1 size=4 +163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +163: test target = O[C@H](F)CCl query = O[C@@H](F)C useChirality = 1 +163: res sub = 0 size=0 +163: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds +163: test target = OC(F)CCl query = OC(F)C useChirality = 0 +163: res sub = 1 size=4 +163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +163: test target = OC(F)CCl query = OC(F)C useChirality = 1 +163: res sub = 1 size=4 +163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +163: test target = OC(F)CCl query = O[C@H](F)C useChirality = 0 +163: res sub = 1 size=4 +163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +163: test target = OC(F)CCl query = O[C@H](F)C useChirality = 1 +163: res sub = 0 size=0 +163: MCS: [#9] 1 atoms, 0 bonds +163: test target = OC(F)CCl query = O[C@@H](F)C useChirality = 0 +163: res sub = 1 size=4 +163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +163: test target = OC(F)CCl query = O[C@@H](F)C useChirality = 1 +163: res sub = 0 size=0 +163: MCS: [#9] 1 atoms, 0 bonds +163: test target = O[C@H](F)CCl query = O[C@H]C useChirality = 0 +163: res sub = 1 size=3 +163: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds +163: test target = O[C@H](F)CCl query = O[C@H]C useChirality = 1 +163: res sub = 1 size=3 +163: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds +163: test target = O[C@H](F)CCl query = O[C@@H]C useChirality = 0 +163: res sub = 1 size=3 +163: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds +163: test target = O[C@H](F)CCl query = O[C@@H]C useChirality = 1 +163: res sub = 1 size=3 +163: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds +163: +163: 0. <<<<<<<<< actual MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds >>>>>>> +163: test target = CC[C@H](F)Cl query = CC[C@H] useChirality = 0 +163: res sub = 1 size=3 +163: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds +163: test target = CC[C@H](F)Cl query = CC[C@H] useChirality = 1 +163: res sub = 1 size=3 +163: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds +163: done +211: 32 The length of bond 16 between atoms 16 and 1 exceeds a configured limit +195: ............[14:17:49] Explicit valence for atom # 1 C, 5, is greater than permitted +143: [14:17:49] done +143: [14:17:49] ------------------------------------- +143: [14:17:49] Testing GitHubIssue62. +211: 8388608 One or more metal atoms were disconnected. +211: 33554432 One or more disconnected fragments (e.g., counterions) were removed. +211: 67108864 The protonation state was adjusted. +143: [14:17:49] beta-lactam 39.6387 +143: [14:17:49] cyclopropanone 174.698 +143: [14:17:49] aziridine 337.986 +143: [14:17:49] aziridinone 115.248 +143: [14:17:49] isobutene 2.48217 +172: .... +172: ---------------------------------------------------------------------- +172: Ran 14 tests in 5.471s +172: +172: OK +211: 16777216 The representation of some functional groups was adjusted. +211: 67108864 The protonation state was adjusted. +143: [14:17:49] acetone 1.91788 +143: [14:17:49] cyclopentanone 10.1648 +211: 16777216 The representation of some functional groups was adjusted. +211: 67108864 The protonation state was adjusted. +160: =============================================================================== +160: All tests passed (6857 assertions in 116 test cases) +160: +174/236 Test #160: moldraw2DTestCatch ..................... Passed 8.07 sec +test 214 + Start 214: pyScaffoldNetwork + +214: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ScaffoldNetwork/Wrap/testScaffoldNetwork.py" +214: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap +214: Test timeout computed to be: 1500 +143: [14:17:49] cyclopropene 99.4921 +143: [14:17:49] cyclobutene 41.0156 +143: [14:17:49] cyclopropane 267.236 +195: ......[14:17:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +195: [14:17:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +195: [14:17:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +195: [14:17:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +211: 16777216 The representation of some functional groups was adjusted. +143: [14:17:49] gamma-lactam 15.7471 +195: .inWedges: [H]C12C3([H])C4([H])C1([H])C1([H])C2([H])C3([H])C41[H] |(-0.612,-0.6446,0.635;0.0021,-0.0041,0.002;-0.0187,1.5258,0.0104;-0.6498,2.1424,0.6504;1.5111,1.5466,-0.0041;2.1372,2.1804,0.624;1.5319,0.0168,-0.0125;2.175,-0.6067,0.6086;1.5173,0.025,-1.5424;2.1484,-0.5936,-2.1805;-0.0125,0.0041,-1.5279;-0.6405,-0.6297,-2.154;-0.0333,1.534,-1.5195;-0.6783,2.1574,-2.1387;1.4965,1.5548,-1.534;2.1106,2.1972,-2.1651)| +186: bulk +211: 16777216 The representation of some functional groups was adjusted. +211: 67108864 The protonation state was adjusted. +211: 16777216 The representation of some functional groups was adjusted. +211: 67108864 The protonation state was adjusted. +211: 16777216 The representation of some functional groups was adjusted. +211: 67108864 The protonation state was adjusted. +211: 16777216 The representation of some functional groups was adjusted. +211: 67108864 The protonation state was adjusted. +143: [14:17:49] trans-2,3-diphenylcyclopropan-1-one 203.398 +148: [14:17:49] Molecule does not have explicit Hs. Consider calling AddHs() +175/236 Test #172: pyRascalMCES ........................... Passed 6.74 sec +test 215 + Start 215: pyScaffoldNetworkPickling -205: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molValidateTest -205: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize -205: Test timeout computed to be: 1500 -195: ........[17:55:23] non-ring atom 0 marked aromatic -195: [17:55:23] non-ring atom 0 marked aromatic -195: [17:55:23] +215: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ScaffoldNetwork/Wrap/testPickleScaffoldNetwork.py" +215: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap +215: Test timeout computed to be: 1500 +211: 8388608 One or more metal atoms were disconnected. +211: 33554432 One or more disconnected fragments (e.g., counterions) were removed. +195: ........[14:17:49] non-ring atom 0 marked aromatic +195: [14:17:49] non-ring atom 0 marked aromatic +195: [14:17:49] 195: 195: **** 195: Range Error @@ -31086,9 +31485,9 @@ 195: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 195: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 195: 3# RDKit::RWMol::removeAtom(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -195: 4# 0x00007F81A8084A70 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 4# 0x00007FE6ACC84A70 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -195: 6# 0x00007F81AA8A162C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 6# 0x00007FE6AF4E762C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 195: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -31099,17 +31498,17 @@ 195: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 195: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 195: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 17# 0x00007F81A7FB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 18# 0x00007F81A7FB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 19# 0x00007F81A7FB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 20# 0x00007F81A7FB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 21# 0x00007F81A7FB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 17# 0x00007FE6ACBB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 18# 0x00007FE6ACBB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 19# 0x00007FE6ACBB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 20# 0x00007FE6ACBB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 21# 0x00007FE6ACBB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 26# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -195: 27# 0x00007F81AA89E3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 27# 0x00007FE6AF4E43C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 28# _PyObject_MakeTpCall in /usr/bin/python3 195: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 30# 0x00000000005CD3C9 in /usr/bin/python3 @@ -31141,25 +31540,17 @@ 195: 56# 0x00000000006B921E in /usr/bin/python3 195: 57# Py_RunMain in /usr/bin/python3 195: 58# Py_BytesMain in /usr/bin/python3 -195: 59# 0x00007F81AB07BCA8 in /lib/x86_64-linux-gnu/libc.so.6 +195: 59# 0x00007FE6AFCC1CA8 in /lib/x86_64-linux-gnu/libc.so.6 195: 60# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 195: 61# _start in /usr/bin/python3 195: ---------- 195: **** 195: -195: [17:55:23] non-ring atom 0 marked aromatic -195: [17:55:23] non-ring atom 0 marked aromatic -195: [17:55:23] +195: [14:17:49] non-ring atom 0 marked aromatic +195: [14:17:49] non-ring atom 0 marked aromatic +195: [14:17:49] 195: 195: **** -164/236 Test #197: pyTestTrajectory ....................... Passed 1.01 sec -test 206 - Start 206: molChargeTest - -206: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molChargeTest -206: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize -206: Test timeout computed to be: 1500 -204: [17:55:23] Can't kekulize mol. Unkekulized atoms: 3 7 8 9 195: Range Error 195: idx 195: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp @@ -31170,9 +31561,9 @@ 195: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 195: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 195: 3# RDKit::RWMol::removeAtom(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -195: 4# 0x00007F81A8084A70 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 4# 0x00007FE6ACC84A70 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -195: 6# 0x00007F81AA8A162C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 6# 0x00007FE6AF4E762C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 195: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -31183,17 +31574,17 @@ 195: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 195: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 195: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 17# 0x00007F81A7FB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 18# 0x00007F81A7FB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 19# 0x00007F81A7FB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 20# 0x00007F81A7FB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 21# 0x00007F81A7FB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 17# 0x00007FE6ACBB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 18# 0x00007FE6ACBB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 19# 0x00007FE6ACBB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 20# 0x00007FE6ACBB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 21# 0x00007FE6ACBB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 26# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -195: 27# 0x00007F81AA89E3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 27# 0x00007FE6AF4E43C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 28# _PyObject_MakeTpCall in /usr/bin/python3 195: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 30# 0x00000000005CD3C9 in /usr/bin/python3 @@ -31225,584 +31616,180 @@ 195: 56# 0x00000000006B921E in /usr/bin/python3 195: 57# Py_RunMain in /usr/bin/python3 195: 58# Py_BytesMain in /usr/bin/python3 -195: 59# 0x00007F81AB07BCA8 in /lib/x86_64-linux-gnu/libc.so.6 +195: 59# 0x00007FE6AFCC1CA8 in /lib/x86_64-linux-gnu/libc.so.6 195: 60# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 195: 61# _start in /usr/bin/python3 195: ---------- 195: **** 195: -160: file testFlexiCanvas.2a.png gave hash 1389326866U not the expected 2609920321U -160: file testFlexiCanvas.2b.png gave hash 614693993U not the expected 3615599154U -160: file testFlexiCanvas.3.svg gave hash 236661785U not the expected 3544316588U -195: ...............[17:55:23] WARNING: the onlyHeavy argument to mol.GetNumAtoms() has been deprecated. Please use the onlyExplicit argument instead or mol.GetNumHeavyAtoms() if you want the heavy atom count. -195: [17:55:23] WARNING: the onlyHeavy argument to mol.GetNumAtoms() has been deprecated. Please use the onlyExplicit argument instead or mol.GetNumHeavyAtoms() if you want the heavy atom count. -151: 976734370 -151: =============================================================================== -151: All tests passed (73 assertions in 3 test cases) -151: -165/236 Test #151: molAlignCatchTest ...................... Passed 3.56 sec -test 207 - Start 207: molTautomerTest - -207: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molTautomerTest -207: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize -207: Test timeout computed to be: 1500 -205: ERROR: [FeaturesValidation] Query atom 0 is not allowed -205: ERROR: [FeaturesValidation] Dummy atom 0 is not allowed -205: ERROR: [FeaturesValidation] Query bond 0 is not allowed -205: ERROR: [FeaturesValidation] Bond 0 of aromatic type is not allowed -205: ERROR: [FeaturesValidation] Bond 1 of aromatic type is not allowed -205: ERROR: [FeaturesValidation] Bond 2 of aromatic type is not allowed -205: ERROR: [FeaturesValidation] Bond 3 of aromatic type is not allowed -205: ERROR: [FeaturesValidation] Bond 5 of aromatic type is not allowed -205: ERROR: [FeaturesValidation] Bond 6 of aromatic type is not allowed -205: ERROR: [FeaturesValidation] Bond 2 of dative type is not allowed -205: ERROR: [FeaturesValidation] Bond 3 of dative type is not allowed -205: ERROR: [FeaturesValidation] Atom 2 with alias 'CF3' is not allowed -205: ERROR: [FeaturesValidation] Enhanced stereochemistry features are not allowed -205: ERROR: [StereoValidation] Atom 3 has both unknown and wedged/dashed stereo bonds. -205: here -205: ERROR: [StereoValidation] Bond 3 has assigned stereo type, but unexpected bond order. -205: there -205: ERROR: [StereoValidation] Atom 0 has stereo bonds, but less than 3 explicit substituents. -160: file testGithub4764.sz1.svg gave hash 2364628953U not the expected 3611125861U -160: file testGithub4764.sz2.svg gave hash 1490175526U not the expected 1936114454U -160: file testGithub4764.sz3.svg gave hash 1662881340U not the expected 2712214121U -166/236 Test #205: molValidateTest ........................ Passed 0.13 sec -test 208 - Start 208: molStandardizeSmallTest - -208: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeSmallTest -208: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize -208: Test timeout computed to be: 1500 -160: file testGithub4764.sz1.png gave hash 517897906U not the expected 2179222277U -69: [17:55:23] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -69: [17:55:23] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -69: [17:55:23] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -69: [17:55:23] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -204: [17:55:23] Initializing Normalizer -204: [17:55:23] Running Normalizer -204: [17:55:23] Rule applied: BrokenazidetoN=N+=N- -204: [17:55:23] Initializing Normalizer -204: [17:55:23] Running Normalizer -204: [17:55:23] Initializing Normalizer -204: [17:55:23] Running Normalizer -167/236 Test #204: molNormalizeTest ....................... Passed 0.17 sec -69: [17:55:23] deprecated group abbreviation ignored on line 24 -test 209 - Start 209: molFragmentTest - -209: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molFragmentTest -209: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize -209: Test timeout computed to be: 1500 -195: ..............[17:55:23] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -195: [17:55:23] Explicit valence for atom # 1 C, 5, is greater than permitted -168/236 Test #206: molChargeTest .......................... Passed 0.14 sec -test 210 - Start 210: molStandardizeCatchTest - -210: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeCatchTest -210: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize -210: Test timeout computed to be: 1500 -69: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] -69: [17:55:23] -69: -69: **** -69: Post-condition Violation -69: Element 'Mv' not found -69: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h -69: Failed Expression: anum > -1 -69: ---------- -69: Stacktrace: -69: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -69: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -69: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 3# 0x00007FCE1F4C8531 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 4# 0x00007FCE1F4D1DFA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 5# 0x00007FCE1F4D217D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 6# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 8# RDKit::v2::FileParsers::MolFromMolFile(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 9# 0x000055BED1229C15 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 10# 0x000055BED1290372 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 11# 0x000055BED12109A3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 12# 0x00007FCE1EA33CA8 in /lib/x86_64-linux-gnu/libc.so.6 -69: 13# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -69: 14# 0x000055BED1210AD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: ---------- -69: **** -69: -201: [17:55:23] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. -201: [17:55:23] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. -201: [17:55:23] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. -201: .[17:55:23] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. -201: [17:55:23] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. -201: [17:55:23] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. -201: ...[17:55:23] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. -201: [17:55:23] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. -201: [17:55:23] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. -201: . -201: ---------------------------------------------------------------------- -201: Ran 5 tests in 0.014s -201: -201: OK -160: file testGithub4764.sz2.png gave hash 2568067924U not the expected 444262090U -169/236 Test #201: pyTestPropertyLists .................... Passed 0.33 sec -test 211 - Start 211: molStandardizePipelineTest - -211: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizePipelineTest -211: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize -211: Test timeout computed to be: 1500 -170/236 Test #208: molStandardizeSmallTest ................ Passed 0.10 sec -test 212 - Start 212: pyMolStandardize - -212: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Wrap/testMolStandardize.py" -212: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap -212: Test timeout computed to be: 1500 -160: file testGithub4764.sz3.png gave hash 2910755141U not the expected 3567162200U -209: [17:55:24] SMARTS Parse Error: syntax error while parsing: [Cl -209: [17:55:24] SMARTS Parse Error: Failed parsing SMARTS '[Cl' for input: '[Cl' -171/236 Test #209: molFragmentTest ........................ Passed 0.09 sec -test 213 - Start 213: testScaffoldNetwork - -213: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/testScaffoldNetwork -213: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork -213: Test timeout computed to be: 1500 -211: Randomness seeded to: 1853700624 -211: 1 Counts line too short: '' on line4 -211: 1 Could not instantiate a valid molecule from input -211: 8 Molecule has no atoms -211: [17:55:24] Explicit valence for atom # 1 N, 4, is greater than permitted -211: [17:55:24] Explicit valence for atom # 1 N, 4, is greater than permitted -160: file github5383_1.svg gave hash 4241964660U not the expected 1815941817U -211: 8 Explicit valence for atom # 1 N, 4, is greater than permitted -211: 128 An error occurred while preparing the molecule for standardization. -160: file github5383_2.svg gave hash 2560846108U not the expected 0U -211: 8 The molecule contains an unknown isotope: 3C -211: 4 Query atom 0 is not allowed -211: 4 Bond 0 of aromatic type is not allowed -211: 4 Bond 1 of aromatic type is not allowed -211: 4 Bond 2 of aromatic type is not allowed -211: 4 Bond 3 of aromatic type is not allowed -211: 4 Bond 5 of aromatic type is not allowed -211: 4 Bond 6 of aromatic type is not allowed -160: file github5383_1.png gave hash 1118153320U not the expected 2893520928U -211: 4 Bond 2 of dative type is not allowed -211: 4 Bond 3 of dative type is not allowed -211: 4 Enhanced stereochemistry features are not allowed -160: file acs1996_1.png gave hash 1014030062U not the expected 2329725800U -211: 8 The radical at atom 0 is not allowed -211: [17:55:24] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -160: file acs1996_2.png gave hash 1604110899U not the expected 2996350718U -211: 16 The molecule includes non-null Z coordinates -160: file acs1996_3.svg gave hash 3058522544U not the expected 879041204U -211: 32 Atom 0 too close to bond 2 -211: 32 The length of bond 3 between atoms 0 and 3 exceeds a configured limit -111: [17:55:24] done -111: [17:55:24] ------------------------------------- -111: [17:55:24] Test Issue252: Bad definitions for Crippen atom types. -211: 64 Atom 0 has 3 explicit substituents and multiple stereo bonds -111: [17:55:24] done -111: [17:55:24] ------------------------------------- -111: [17:55:24] Test calculation of ChiVs. -211: 64 Atom 0 has adjacent stereo bonds with like orientation -211: [17:55:24] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -211: 16 The molecule includes non-null Z coordinates -211: 64 Atom 0 has adjacent stereo bonds with like orientation -111: [17:55:24] done -111: [17:55:24] ------------------------------------- -111: [17:55:24] Test calculation of ChiNs. -160: [17:55:24] 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. -111: [17:55:24] done -111: [17:55:24] ------------------------------------- -111: [17:55:24] Test calculation of HallKierAlpha. -111: [17:55:24] done -111: [17:55:24] ------------------------------------- -111: [17:55:24] Test calculation of Kappa1. -211: 32 The length of bond 16 between atoms 16 and 1 exceeds a configured limit -202: . -202: ---------------------------------------------------------------------- -202: Ran 1 test in 0.029s -202: -202: OK -111: [17:55:24] done -111: [17:55:24] ------------------------------------- -111: [17:55:24] Test calculation of Kappa2. -111: [17:55:24] done -111: [17:55:24] ------------------------------------- -111: [17:55:24] Test calculation of Kappa3. -111: [17:55:24] done -111: [17:55:24] ------------------------------------- -111: [17:55:24] Test Crippen atom type calculations. -111: [17:55:24] done -111: [17:55:24] ------------------------------------- -111: [17:55:24] Test ring descriptors +211: 67108864 The protonation state was adjusted. 211: 8388608 One or more metal atoms were disconnected. 211: 33554432 One or more disconnected fragments (e.g., counterions) were removed. 211: 67108864 The protonation state was adjusted. -211: 16777216 The representation of some functional groups was adjusted. -211: 67108864 The protonation state was adjusted. +143: [14:17:49] cis-2,3-diphenylcyclopropan-1-one 206.852 200: .s. 200: ---------------------------------------------------------------------- -200: Ran 3 tests in 0.183s +200: Ran 3 tests in 0.291s 200: 200: OK (skipped=1) 200: Testing Smiles and SD MultithreadedMolSupplier -160: file bond_highlights_8.svg gave hash 3610726614U not the expected 3119784980U -111: [17:55:24] done -111: [17:55:24] ------------------------------------- -111: [17:55:24] Test other count descriptors. -111: [17:55:24] done -111: [17:55:24] ------------------------------------- -111: [17:55:24] Test MQN -211: 16777216 The representation of some functional groups was adjusted. -211: 67108864 The protonation state was adjusted. -211: 16777216 The representation of some functional groups was adjusted. -111: [17:55:24] done -111: [17:55:24] ------------------------------------- -111: [17:55:24] Test GitHub Issue 56. -111: [17:55:24] WARNING: not removing hydrogen atom without neighbors -111: [17:55:24] WARNING: not removing hydrogen atom without neighbors -111: [17:55:24] WARNING: not removing hydrogen atom without neighbors -111: [17:55:24] WARNING: not removing hydrogen atom without neighbors -111: [17:55:24] done -111: [17:55:24] ------------------------------------- -111: [17:55:24] Test Github92: Bad Crippen atom type for pyrrole H. -211: 16777216 The representation of some functional groups was adjusted. -211: 67108864 The protonation state was adjusted. -111: [17:55:24] done -111: [17:55:24] ------------------------------------- -111: [17:55:24] Test Github362: order dependence in Kier-Hall descriptors. -111: [17:55:24] done -111: [17:55:24] ------------------------------------- -111: [17:55:24] Test calculation of spiro and bridgehead counts. -111: [17:55:24] done -111: [17:55:24] ------------------------------------- -111: [17:55:24] Test Github694: ExactMolWt ignoring the mass of the electron -111: [17:55:24] done -111: [17:55:24] ------------------------------------- -111: [17:55:24] Testing Properties and KitchenSink -211: 16777216 The representation of some functional groups was adjusted. -211: 67108864 The protonation state was adjusted. -211: 16777216 The representation of some functional groups was adjusted. -211: 67108864 The protonation state was adjusted. -111: [17:55:24] ---Caught keyerror (bad property name)--- -211: 16777216 The representation of some functional groups was adjusted. -111: [17:55:24] ------------------------------------- -111: [17:55:24] Test USR Descriptor -211: 67108864 The protonation state was adjusted. -111: [17:55:24] done -111: [17:55:24] ------------------------------------- -111: [17:55:24] Test Github #1702: AUTOCORR2D.h not installed unless RDK_BUILD_DESCRIPTORS3D but is required -111: [17:55:24] done -111: [17:55:24] ------------------------------------- -111: [17:55:24] Test Github #1973: support P and S terms for TPSA calculation -211: 8388608 One or more metal atoms were disconnected. -211: 33554432 One or more disconnected fragments (e.g., counterions) were removed. -111: [17:55:24] done -111: [17:55:24] ------------------------------------- -111: [17:55:24] Test Github #2948: Empty molecule has non-zero LabuteASA -111: [17:55:24] done -172/236 Test #111: testDescriptors ........................ Passed 4.46 sec -test 214 - Start 214: pyScaffoldNetwork - -214: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ScaffoldNetwork/Wrap/testScaffoldNetwork.py" -214: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap -214: Test timeout computed to be: 1500 -211: 67108864 The protonation state was adjusted. -211: 8388608 One or more metal atoms were disconnected. -211: 33554432 One or more disconnected fragments (e.g., counterions) were removed. -211: 67108864 The protonation state was adjusted. 211: 8388608 One or more metal atoms were disconnected. 211: 33554432 One or more disconnected fragments (e.g., counterions) were removed. 211: 67108864 The protonation state was adjusted. +143: [14:17:49] 2,3-diphenylcyclopropa-2-en-1-one 20.0443 211: 8388608 One or more metal atoms were disconnected. 211: 33554432 One or more disconnected fragments (e.g., counterions) were removed. 211: 67108864 The protonation state was adjusted. +143: [14:17:49] cyclopropylidencyclobutane 218.879 +195: ...............[14:17:49] WARNING: the onlyHeavy argument to mol.GetNumAtoms() has been deprecated. Please use the onlyExplicit argument instead or mol.GetNumHeavyAtoms() if you want the heavy atom count. +195: [14:17:49] WARNING: the onlyHeavy argument to mol.GetNumAtoms() has been deprecated. Please use the onlyExplicit argument instead or mol.GetNumHeavyAtoms() if you want the heavy atom count. 211: 8388608 One or more metal atoms were disconnected. 211: 33554432 One or more disconnected fragments (e.g., counterions) were removed. 211: 67108864 The protonation state was adjusted. 211: 16777216 The "wavy" style of bond 4 was removed -211: 16777216 Double bond 1 was assigned an undefined/unknown stereochemical configuration -211: 16777216 The "wavy" style of bond 2 was removed -211: 16777216 Double bond 2 was assigned an undefined/unknown stereochemical configuration -211: 16777216 The "wavy" style of bond 1 was removed -211: 16777216 Double bond 2 was assigned an undefined/unknown stereochemical configuration -211: 16777216 The "wavy" style of bond 1 was removed -211: 16777216 The "wavy" style of bond 4 was removed -211: 16777216 Double bond 2 was assigned an undefined/unknown stereochemical configuration -211: 16777216 The "wavy" style of bond 3 was removed -173/236 Test #202: pyCDXMLTest ............................ Passed 0.54 sec -test 215 - Start 215: pyScaffoldNetworkPickling - -215: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ScaffoldNetwork/Wrap/testPickleScaffoldNetwork.py" -215: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap -215: Test timeout computed to be: 1500 -211: 16777216 The representation of some functional groups was adjusted. -160: file test_github6112.svg gave hash 3865338574U not the expected 3278777629U -211: [17:55:24] Can't kekulize mol. Unkekulized atoms: 2 3 5 -211: =============================================================================== -211: All tests passed (268 assertions in 5 test cases) -211: -174/236 Test #211: molStandardizePipelineTest ............. Passed 0.24 sec +176/236 Test #200: pyTestMultithreadedMolSupplier ......... Passed 1.90 sec test 216 Start 216: testMolEnumerator 216: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/testMolEnumerator 216: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator 216: Test timeout computed to be: 1500 -69: [17:55:24] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -69: [17:55:24] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -175/236 Test #200: pyTestMultithreadedMolSupplier ......... Passed 0.62 sec +211: 16777216 Double bond 1 was assigned an undefined/unknown stereochemical configuration +211: 16777216 The "wavy" style of bond 2 was removed +189: .................... +189: ---------------------------------------------------------------------- +189: Ran 20 tests in 2.387s +189: +189: OK +211: 16777216 Double bond 2 was assigned an undefined/unknown stereochemical configuration +211: 16777216 The "wavy" style of bond 1 was removed +211: 16777216 Double bond 2 was assigned an undefined/unknown stereochemical configuration +211: 16777216 The "wavy" style of bond 1 was removed +177/236 Test #189: pyRGroupDecomposition .................. Passed 3.47 sec test 217 Start 217: pyMolEnumerator 217: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/Wrap/rough_test.py" 217: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap 217: Test timeout computed to be: 1500 -148: [17:55:24] Molecule does not have explicit Hs. Consider calling AddHs() -216: Randomness seeded to: 3948613973 -216: [17:55:24] can only enumerate SRUs with CONNECT=HT or CONNECT=HH -210: Randomness seeded to: 3599340846 -210: * - * - * - * m1 -216: =============================================================================== -216: All tests passed (321 assertions in 16 test cases) -216: -176/236 Test #216: testMolEnumerator ...................... Passed 0.12 sec +214: ....... +214: ---------------------------------------------------------------------- +214: Ran 7 tests in 0.048s +214: +214: OK +143: [14:17:49] diphenylmethylidencyclobutane 79.6139 +143: [14:17:49] done +143: [14:17:49] ------------------------------------- +143: [14:17:49] Test Github Issue 613: UFF Atom type not properly assigned to lanthanides. +143: [14:17:49] done +143: [14:17:49] ------------------------------------- +143: [14:17:49] Test square planar complexes +143: [14:17:49] done +143: [14:17:49] ------------------------------------- +143: [14:17:49] Test octahedral complexes +143: [14:17:49] done +211: 16777216 The "wavy" style of bond 4 was removed +211: 16777216 Double bond 2 was assigned an undefined/unknown stereochemical configuration +211: 16777216 The "wavy" style of bond 3 was removed +216: Randomness seeded to: 3779360792 +216: [14:17:49] can only enumerate SRUs with CONNECT=HT or CONNECT=HH +178/236 Test #143: testUFFForceFieldHelpers ............... Passed 9.67 sec test 218 Start 218: testAbbreviations 218: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/testAbbreviations 218: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations 218: Test timeout computed to be: 1500 -210: * - * - * - * m2 -210: * - * - * - * m1 -210: * - * - * - * m2 -210: [17:55:24] Can't kekulize mol. Unkekulized atoms: 3 7 -148: [17:55:24] Molecule does not have explicit Hs. Consider calling AddHs() -69: ---------------------------------- -69: ---------------------------------- -69: [17:55:24] -69: -69: **** -69: Pre-condition Violation -69: rlabel out of range for MDL files -69: Violation occurred on line 863 in file ./Code/GraphMol/Atom.cpp -69: Failed Expression: rlabel >= 0 && rlabel < 100 -69: ---------- -69: Stacktrace: -69: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -69: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -69: 2# RDKit::setAtomRLabel(RDKit::Atom*, int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -69: 3# 0x000055BED1236FFF in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 4# 0x000055BED12903EA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 5# 0x000055BED12109A3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 6# 0x00007FCE1EA33CA8 in /lib/x86_64-linux-gnu/libc.so.6 -69: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -69: 8# 0x000055BED1210AD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: ---------- -69: **** -69: -69: [17:55:24] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -210: [17:55:24] Can't kekulize mol. Unkekulized atoms: 3 8 -210: [17:55:24] Can't kekulize mol. Unkekulized atoms: 2 3 4 -218: Randomness seeded to: 3924931315 -218: [17:55:24] SMARTS Parse Error: syntax error while parsing: *fail -218: [17:55:24] SMARTS Parse Error: Failed parsing SMARTS '*fail' for input: '*fail' -218: [17:55:24] no suitable SubstanceGroups found -218: =============================================================================== -218: All tests passed (195 assertions in 12 test cases) -218: -177/236 Test #218: testAbbreviations ...................... Passed 0.09 sec +211: 16777216 The representation of some functional groups was adjusted. +179/236 Test #214: pyScaffoldNetwork ...................... Passed 0.47 sec test 219 Start 219: pyAbbreviations 219: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Abbreviations/Wrap/testAbbreviations.py" 219: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/Wrap 219: Test timeout computed to be: 1500 -195: ............................[17:55:24] unable to set wavy bonds for double bonds: 3 -195: .............[17:55:24] -195: -195: **** -195: Range Error -195: idx -195: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp -195: Failed Expression: 6 < 5 -195: ---------- -195: Stacktrace: -195: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -195: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -195: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -195: 3# RDKit::RWMol::removeAtom(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -195: 4# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -195: 6# 0x00007F81AA8A162C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -195: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -195: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so -195: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so -195: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so -195: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so -195: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so -195: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so -195: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so -195: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so -195: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 17# 0x00007F81A7FB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 18# 0x00007F81A7FB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 19# 0x00007F81A7FB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 20# 0x00007F81A7FB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 21# 0x00007F81A7FB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so -195: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so -195: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so -195: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so -195: 26# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -195: 27# 0x00007F81AA89E3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -195: 28# _PyObject_MakeTpCall in /usr/bin/python3 -195: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 -195: 30# 0x00000000005CD3C9 in /usr/bin/python3 -195: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 -195: 32# 0x0000000000690C6F in /usr/bin/python3 -195: 33# 0x000000000062D590 in /usr/bin/python3 -195: 34# _PyObject_MakeTpCall in /usr/bin/python3 -195: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 -195: 36# 0x00000000005CD3C9 in /usr/bin/python3 -195: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 -195: 38# 0x0000000000690C6F in /usr/bin/python3 -195: 39# 0x000000000062D590 in /usr/bin/python3 -195: 40# _PyObject_MakeTpCall in /usr/bin/python3 -195: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 -195: 42# 0x00000000005CD3C9 in /usr/bin/python3 -195: 43# _PyEval_EvalFrameDefault in /usr/bin/python3 -195: 44# 0x0000000000690C6F in /usr/bin/python3 -195: 45# 0x000000000062D590 in /usr/bin/python3 -195: 46# _PyObject_MakeTpCall in /usr/bin/python3 -195: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 -195: 48# 0x00000000005A090C in /usr/bin/python3 -195: 49# _PyObject_MakeTpCall in /usr/bin/python3 -195: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 -195: 51# PyEval_EvalCode in /usr/bin/python3 -195: 52# 0x00000000006AB8D1 in /usr/bin/python3 -195: 53# 0x00000000006A899C in /usr/bin/python3 -195: 54# 0x00000000006B9943 in /usr/bin/python3 -195: 55# 0x00000000006B93E3 in /usr/bin/python3 -195: 56# 0x00000000006B921E in /usr/bin/python3 -195: 57# Py_RunMain in /usr/bin/python3 -195: 58# Py_BytesMain in /usr/bin/python3 -195: 59# 0x00007F81AB07BCA8 in /lib/x86_64-linux-gnu/libc.so.6 -195: 60# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -195: 61# _start in /usr/bin/python3 -195: ---------- -195: **** -195: -148: [17:55:24] Molecule does not have explicit Hs. Consider calling AddHs() -217: ... -217: ---------------------------------------------------------------------- -217: Ran 3 tests in 0.014s -217: -217: OK -215: . -215: ---------------------------------------------------------------------- -215: Ran 1 test in 0.014s -215: -215: OK -178/236 Test #215: pyScaffoldNetworkPickling .............. Passed 0.42 sec +216: =============================================================================== +216: All tests passed (321 assertions in 16 test cases) +216: +180/236 Test #216: testMolEnumerator ...................... Passed 0.15 sec test 220 Start 220: generalizedSubstructCatch 220: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/generalizedSubstructCatch 220: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct 220: Test timeout computed to be: 1500 -179/236 Test #217: pyMolEnumerator ........................ Passed 0.40 sec +211: [14:17:49] Can't kekulize mol. Unkekulized atoms: 2 3 5 +69: [14:17:49] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas +69: [14:17:49] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' +211: =============================================================================== +211: All tests passed (268 assertions in 5 test cases) +211: +181/236 Test #211: molStandardizePipelineTest ............. Passed 1.18 sec test 221 Start 221: pyGeneralizedSubstruct 221: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/GeneralizedSubstruct/Wrap/testGeneralizedSubstruct.py" 221: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap 221: Test timeout computed to be: 1500 -29: Checking against /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -148: [17:55:24] Molecule does not have explicit Hs. Consider calling AddHs() -214: ....... -214: ---------------------------------------------------------------------- -214: Ran 7 tests in 0.048s -214: -214: OK -146: validating reference data -180/236 Test #214: pyScaffoldNetwork ...................... Passed 0.56 sec +218: Randomness seeded to: 2482076054 +218: [14:17:49] SMARTS Parse Error: syntax error while parsing: *fail +218: [14:17:49] SMARTS Parse Error: Failed parsing SMARTS '*fail' for input: '*fail' +195: ..............[14:17:49] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +195: [14:17:49] Explicit valence for atom # 1 C, 5, is greater than permitted +218: [14:17:49] no suitable SubstanceGroups found +218: =============================================================================== +218: All tests passed (195 assertions in 12 test cases) +218: +182/236 Test #218: testAbbreviations ...................... Passed 0.15 sec test 222 Start 222: testMolProcessing 222: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing/testMolProcessing 222: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing 222: Test timeout computed to be: 1500 -69: [17:55:24] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas -69: [17:55:24] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' -160: file AtropManyChiralsEnhanced.svg gave hash 3443464321U not the expected 2256768013U -29: All 191 tests passed -69: [17:55:24] Empty atom list: 'M ALS 1 0 F' on line 8. -169: ......... -169: ---------------------------------------------------------------------- -169: Ran 9 tests in 3.716s -169: -169: OK -181/236 Test #69: fileParsersTest1 ....................... Passed 5.40 sec +148: [14:17:49] Molecule does not have explicit Hs. Consider calling AddHs() +69: [14:17:49] Empty atom list: 'M ALS 1 0 F' on line 8. +183/236 Test #69: fileParsersTest1 ....................... Passed 12.16 sec test 223 Start 223: pyMolProcessing 223: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolProcessing/Wrap/testMolProcessing.py" 223: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing/Wrap 223: Test timeout computed to be: 1500 -219: ....... -219: ---------------------------------------------------------------------- -219: Ran 7 tests in 0.023s -219: -219: OK -163: [17:55:24] The provided InitialSeed is not an MCS and will be ignored -182/236 Test #169: pyMMPA ................................. Passed 4.08 sec +220: Randomness seeded to: 3754295253 +220: =============================================================================== +220: All tests passed (486 assertions in 10 test cases) +220: +184/236 Test #220: generalizedSubstructCatch .............. Passed 0.34 sec test 224 Start 224: testMIF 224: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInteractionFields/testMIF 224: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInteractionFields 224: Test timeout computed to be: 1500 -12: .................. -12: ---------------------------------------------------------------------- -12: Ran 18 tests in 5.464s -12: -12: OK -148: [17:55:24] Molecule does not have explicit Hs. Consider calling AddHs() -183/236 Test #219: pyAbbreviations ........................ Passed 0.43 sec +217: ... +217: ---------------------------------------------------------------------- +217: Ran 3 tests in 0.028s +217: +217: OK +224: Randomness seeded to: 930002370 +224: =============================================================================== +224: All tests passed (27926 assertions in 8 test cases) +224: +185/236 Test #224: testMIF ................................ Passed 0.12 sec test 225 Start 225: pyMIF 225: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInteractionFields/Wrap/testMIF.py" 225: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInteractionFields/Wrap 225: Test timeout computed to be: 1500 -184/236 Test #12: pyBV ................................... Passed 8.01 sec +186/236 Test #217: pyMolEnumerator ........................ Passed 0.60 sec test 226 Start 226: testQuery 226: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Query/testQuery 226: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Query 226: Test timeout computed to be: 1500 -224: Randomness seeded to: 4014709562 -224: =============================================================================== -224: All tests passed (27926 assertions in 8 test cases) -224: -29: -29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_dative.smi... -185/236 Test #224: testMIF ................................ Passed 0.08 sec -test 227 - Start 227: testBaseFeatures - -227: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Features/testBaseFeatures -227: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Features -227: Test timeout computed to be: 1500 226: Query 226: Query2 226: Equality @@ -31820,13 +31807,13 @@ 226: XOr 226: pointer and copy foo 226: Set2 -186/236 Test #226: testQuery .............................. Passed 0.01 sec -test 228 - Start 228: testMatCalc +187/236 Test #226: testQuery .............................. Passed 0.04 sec +test 227 + Start 227: testBaseFeatures -228: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/testMatCalc -228: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc -228: Test timeout computed to be: 1500 +227: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Features/testBaseFeatures +227: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Features +227: Test timeout computed to be: 1500 227: ------------------------------------- 227: Basics for ExplicitFeatures. 227: done @@ -31836,7 +31823,18 @@ 227: ------------------------------------- 227: ExplicitFeatures 2D, string type. 227: done -187/236 Test #227: testBaseFeatures ....................... Passed 0.01 sec +188/236 Test #227: testBaseFeatures ....................... Passed 0.03 sec +test 228 + Start 228: testMatCalc + +228: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/testMatCalc +228: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc +228: Test timeout computed to be: 1500 +219: ....... +219: ---------------------------------------------------------------------- +219: Ran 7 tests in 0.023s +219: +219: OK 228: 1.68022e+08 228: 1.73149e+08 228: 1.05549e+08 @@ -31882,143 +31880,124 @@ 228: 9.49496e+07 228: 2.25618e+08 228: 1.30219e+08 +189/236 Test #228: testMatCalc ............................ Passed 0.02 sec test 229 Start 229: pyMatCalc 229: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/DataManip/MetricMatrixCalc/Wrap/testMatricCalc.py" 229: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap 229: Test timeout computed to be: 1500 -188/236 Test #228: testMatCalc ............................ Passed 0.01 sec +190/236 Test #219: pyAbbreviations ........................ Passed 0.65 sec test 230 Start 230: testSimDivPickers 230: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/SimDivPickers/testSimDivPickers 230: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/SimDivPickers 230: Test timeout computed to be: 1500 -230: [17:55:24] ------------------------------------- -230: [17:55:24] Testing github issue 1421: MaxMinPicker picking non-existent element. -230: [17:55:24] Done -230: [17:55:24] ------------------------------------- -230: [17:55:24] Testing github issue 2245: MinMax Diversity picker seeding shows deterministic / non-random behaviour. -230: [17:55:24] Done -189/236 Test #230: testSimDivPickers ...................... Passed 0.01 sec +230: [14:17:50] ------------------------------------- +230: [14:17:50] Testing github issue 1421: MaxMinPicker picking non-existent element. +230: [14:17:50] Done +230: [14:17:50] ------------------------------------- +230: [14:17:50] Testing github issue 2245: MinMax Diversity picker seeding shows deterministic / non-random behaviour. +230: [14:17:50] Done +191/236 Test #230: testSimDivPickers ...................... Passed 0.02 sec test 231 Start 231: pickersTestsCatch 231: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/SimDivPickers/pickersTestsCatch 231: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/SimDivPickers 231: Test timeout computed to be: 1500 -220: Randomness seeded to: 3054091685 -220: =============================================================================== -220: All tests passed (486 assertions in 10 test cases) -220: -190/236 Test #220: generalizedSubstructCatch .............. Passed 0.33 sec +148: [14:17:50] Molecule does not have explicit Hs. Consider calling AddHs() +231: Randomness seeded to: 4048193769 +231: =============================================================================== +231: All tests passed (21267 assertions in 1 test case) +231: +192/236 Test #231: pickersTestsCatch ...................... Passed 0.23 sec test 232 Start 232: pySimDivPickers 232: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/SimDivPickers/Wrap/testPickers.py" 232: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap 232: Test timeout computed to be: 1500 -160: file testGithub_7739_1.svg gave hash 3358510977U not the expected 2615562225U -160: file testGithub_7739_3.svg gave hash 176211825U not the expected 1037942338U -150: *********************************************************** -150: Testing O3AAlign -150: --------------------------------- -150: testMMFFO3A -150: -150: --------------------------------- -150: testMMFFO3A with pre-computed dmat and MolHistogram -150: -150: --------------------------------- -150: testMMFFO3A with constraints -150: -150: --------------------------------- -150: testMMFFO3A with variable weight constraints followed by local-only optimization -150: -150: --------------------------------- -150: testCrippenO3A -150: -150: --------------------------------- -150: testCrippenO3A with pre-computed dmat and MolHistogram -150: -150: --------------------------------- -150: testCrippenO3A with constraints -150: -150: --------------------------------- -150: testCrippenO3A with variable weight constraints followed by local-only optimization -150: -150: --------------------------------- -150: testMMFFO3A multithreading -150: -150: generating reference data -148: [17:55:25] Molecule does not have explicit Hs. Consider calling AddHs() -160: file testGithub_7739_4.svg gave hash 3309264286U not the expected 3549083171U -160: file testSmallReactionCanvas.svg gave hash 3859901121U not the expected 2238356155U -231: Randomness seeded to: 4151509472 -231: =============================================================================== -231: All tests passed (21267 assertions in 1 test case) -231: -191/236 Test #231: pickersTestsCatch ...................... Passed 0.18 sec +150: processing +150: launch :0 +150: launch :1 +150: launch :2 +150: launch :3 +207: [14:17:50] Tautomer enumeration stopped at 292 tautomers: max transforms reached +213: Randomness seeded to: 509482988 +213: =============================================================================== +213: All tests passed (273 assertions in 19 test cases) +213: +215: . +215: ---------------------------------------------------------------------- +215: Ran 1 test in 0.055s +215: +215: OK +193/236 Test #213: testScaffoldNetwork .................... Passed 2.26 sec test 233 Start 233: pyRanker 233: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/ML/InfoTheory/Wrap/testRanker.py" 233: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap 233: Test timeout computed to be: 1500 -212: .....[17:55:25] Tautomer enumeration stopped at 292 tautomers: max transforms reached -186: iterative -207: [17:55:25] Tautomer enumeration stopped at 292 tautomers: max transforms reached -221: ....... -221: ---------------------------------------------------------------------- -221: Ran 7 tests in 0.250s -221: -221: OK -160: =============================================================================== -160: All tests passed (6857 assertions in 116 test cases) -160: -192/236 Test #160: moldraw2DTestCatch ..................... Passed 4.75 sec +232: [14:17:51] the useCache argument is deprecated and ignored +148: [14:17:51] Molecule does not have explicit Hs. Consider calling AddHs() +229: ..... +229: ---------------------------------------------------------------------- +229: Ran 5 tests in 0.587s +229: +229: OK +225: ....... +225: ---------------------------------------------------------------------- +225: Ran 7 tests in 0.262s +225: +225: OK +225: Testing MIF wrapper +194/236 Test #215: pyScaffoldNetworkPickling .............. Passed 1.84 sec +195/236 Test #229: pyMatCalc .............................. Passed 0.87 sec test 234 Start 234: testChemicalFeatures 234: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ChemicalFeatures/testChemicalFeatures 234: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ChemicalFeatures 234: Test timeout computed to be: 1500 -232: [17:55:25] the useCache argument is deprecated and ignored -234: ----------------------------------------- -234: Test1 -234: Done -193/236 Test #234: testChemicalFeatures ................... Passed 0.01 sec test 235 Start 235: pyFeatures 235: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/ChemicalFeatures/Wrap/testFeatures.py" 235: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap 235: Test timeout computed to be: 1500 -212: [17:55:25] Tautomer enumeration stopped at 50 tautomers: max tautomers reached -194/236 Test #221: pyGeneralizedSubstruct ................. Passed 0.66 sec +212: .....[14:17:51] Tautomer enumeration stopped at 292 tautomers: max transforms reached +234: ----------------------------------------- +234: Test1 +234: Done +196/236 Test #234: testChemicalFeatures ................... Passed 0.07 sec test 236 Start 236: pythonProjectTests 236: Test command: /usr/bin/python3 "-m" "pytest" 236: Working Directory: /build/reproducible-path/rdkit-202503.1/Projects 236: Test timeout computed to be: 1500 +197/236 Test #42: resMolSupplierTest ..................... Passed 14.04 sec 223: .. 223: ---------------------------------------------------------------------- -223: Ran 2 tests in 0.258s +223: Ran 2 tests in 1.057s 223: 223: OK -117: =>start test GETAWAY custom -117: [17:55:25] test on : 365 molecules done -195/236 Test #117: testRDFcustom .......................... Passed 5.61 sec -196/236 Test #203: molStandardizeTest ..................... Passed 1.61 sec -225: ....... -225: ---------------------------------------------------------------------- -225: Ran 7 tests in 0.088s -225: -225: OK -225: Testing MIF wrapper -197/236 Test #223: pyMolProcessing ........................ Passed 0.61 sec -233: ..[17:55:25] +232: ...[14:17:51] the useCache argument is deprecated and ignored +232: [14:17:51] the useCache argument is deprecated and ignored +232: .[14:17:51] the useCache argument is deprecated and ignored +198/236 Test #225: pyMIF .................................. Passed 1.17 sec +221: ....... +221: ---------------------------------------------------------------------- +221: Ran 7 tests in 0.610s +221: +221: OK +199/236 Test #223: pyMolProcessing ........................ Passed 1.49 sec +200/236 Test #221: pyGeneralizedSubstruct ................. Passed 1.72 sec +186: bulk, no symmetry +233: ..[14:17:51] 233: 233: **** 233: Invariant Violation @@ -32033,14 +32012,14 @@ 233: 3# RDInfoTheory::getTopNbits(RDInfoTheory::InfoBitRanker*, int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/ML/InfoTheory/rdInfoTheory.so 233: 4# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/ML/InfoTheory/rdInfoTheory.so 233: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -233: 6# 0x00007F06997B862C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +233: 6# 0x00007F4A3349162C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 233: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 233: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 233: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 233: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 233: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 233: 12# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -233: 13# 0x00007F06997B53C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +233: 13# 0x00007F4A3348E3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 233: 14# _PyObject_MakeTpCall in /usr/bin/python3 233: 15# _PyEval_EvalFrameDefault in /usr/bin/python3 233: 16# 0x00000000005CD3C9 in /usr/bin/python3 @@ -32072,7 +32051,7 @@ 233: 42# 0x00000000006B921E in /usr/bin/python3 233: 43# Py_RunMain in /usr/bin/python3 233: 44# Py_BytesMain in /usr/bin/python3 -233: 45# 0x00007F069AF4ECA8 in /lib/x86_64-linux-gnu/libc.so.6 +233: 45# 0x00007F4A346B5CA8 in /lib/x86_64-linux-gnu/libc.so.6 233: 46# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 233: 47# _start in /usr/bin/python3 233: ---------- @@ -32080,69 +32059,121 @@ 233: 233: ... 233: ---------------------------------------------------------------------- -233: Ran 5 tests in 0.027s +233: Ran 5 tests in 0.040s 233: 233: OK -198/236 Test #225: pyMIF .................................. Passed 0.54 sec -232: ...[17:55:25] the useCache argument is deprecated and ignored -232: [17:55:25] the useCache argument is deprecated and ignored -232: .[17:55:25] the useCache argument is deprecated and ignored -199/236 Test #233: pyRanker ............................... Passed 0.34 sec -213: Randomness seeded to: 1126759 -213: =============================================================================== -213: All tests passed (273 assertions in 19 test cases) -213: -200/236 Test #213: testScaffoldNetwork .................... Passed 1.44 sec -189: .................... -189: ---------------------------------------------------------------------- -189: Ran 20 tests in 2.734s -189: -189: OK -201/236 Test #189: pyRGroupDecomposition .................. Passed 3.42 sec -171: Randomness seeded to: 3493846750 -171: /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/data/chembl_1907596.smi -212: .[17:55:25] Tautomer enumeration stopped at 50 tautomers: canceled -212: Enumeration was canceled due to timeout (50 ms) +212: [14:17:51] Tautomer enumeration stopped at 50 tautomers: max tautomers reached +201/236 Test #233: pyRanker ............................... Passed 0.65 sec 235: .. 235: ---------------------------------------------------------------------- -235: Ran 2 tests in 0.004s +235: Ran 2 tests in 0.003s 235: 235: OK 235: Testing ChemicalFeatures Wrapper code: -202/236 Test #235: pyFeatures ............................. Passed 1.58 sec -148: .[17:55:26] Molecule does not have explicit Hs. Consider calling AddHs() -229: ..... -229: ---------------------------------------------------------------------- -229: Ran 5 tests in 1.511s -229: -229: OK -207: [17:55:26] Tautomer enumeration stopped at 292 tautomers: max transforms reached -203/236 Test #229: pyMatCalc .............................. Passed 1.98 sec -207: [17:55:27] Tautomer enumeration stopped at 50 tautomers: max tautomers reached -128: [17:55:27] done -128: [17:55:27] ------------------------------------- -128: [17:55:27] Test GitHub Issue 258: Bad pattern fingerprint for query molecule -128: [17:55:27] done -128: [17:55:27] ------------------------------------- -128: [17:55:27] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. -128: [17:55:27] DEPRECATION WARNING: please use AtomPairGenerator -128: [17:55:27] DEPRECATION WARNING: please use AtomPairGenerator -128: [17:55:27] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:27] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:27] done -128: [17:55:27] ------------------------------------- -128: [17:55:27] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints -128: [17:55:27] done -128: [17:55:27] ------------------------------------- -128: [17:55:27] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 -128: [17:55:27] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:27] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:27] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:27] done -128: [17:55:27] ------------------------------------- -128: [17:55:27] Test unfolded version of RDKFP -128: [17:55:27] ------------------------------------- -128: [17:55:27] Test bitinfo of RDKFP +195: ............................[14:17:51] unable to set wavy bonds for double bonds: 3 +202/236 Test #235: pyFeatures ............................. Passed 0.41 sec +195: .............[14:17:51] +195: +195: **** +195: Range Error +195: idx +195: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp +195: Failed Expression: 6 < 5 +195: ---------- +195: Stacktrace: +195: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +195: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +195: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +195: 3# RDKit::RWMol::removeAtom(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +195: 4# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 6# 0x00007FE6AF4E762C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so +195: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so +195: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so +195: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so +195: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so +195: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so +195: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so +195: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so +195: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 17# 0x00007FE6ACBB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 18# 0x00007FE6ACBB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 19# 0x00007FE6ACBB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 20# 0x00007FE6ACBB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 21# 0x00007FE6ACBB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so +195: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so +195: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so +195: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so +195: 26# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 27# 0x00007FE6AF4E43C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 28# _PyObject_MakeTpCall in /usr/bin/python3 +195: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 +195: 30# 0x00000000005CD3C9 in /usr/bin/python3 +195: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 +195: 32# 0x0000000000690C6F in /usr/bin/python3 +195: 33# 0x000000000062D590 in /usr/bin/python3 +195: 34# _PyObject_MakeTpCall in /usr/bin/python3 +195: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 +195: 36# 0x00000000005CD3C9 in /usr/bin/python3 +195: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 +195: 38# 0x0000000000690C6F in /usr/bin/python3 +195: 39# 0x000000000062D590 in /usr/bin/python3 +195: 40# _PyObject_MakeTpCall in /usr/bin/python3 +195: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 +195: 42# 0x00000000005CD3C9 in /usr/bin/python3 +195: 43# _PyEval_EvalFrameDefault in /usr/bin/python3 +195: 44# 0x0000000000690C6F in /usr/bin/python3 +195: 45# 0x000000000062D590 in /usr/bin/python3 +195: 46# _PyObject_MakeTpCall in /usr/bin/python3 +195: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 +195: 48# 0x00000000005A090C in /usr/bin/python3 +195: 49# _PyObject_MakeTpCall in /usr/bin/python3 +195: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 +195: 51# PyEval_EvalCode in /usr/bin/python3 +195: 52# 0x00000000006AB8D1 in /usr/bin/python3 +195: 53# 0x00000000006A899C in /usr/bin/python3 +195: 54# 0x00000000006B9943 in /usr/bin/python3 +195: 55# 0x00000000006B93E3 in /usr/bin/python3 +195: 56# 0x00000000006B921E in /usr/bin/python3 +195: 57# Py_RunMain in /usr/bin/python3 +195: 58# Py_BytesMain in /usr/bin/python3 +195: 59# 0x00007FE6AFCC1CA8 in /lib/x86_64-linux-gnu/libc.so.6 +195: 60# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +195: 61# _start in /usr/bin/python3 +195: ---------- +195: **** +195: +148: [14:17:51] Molecule does not have explicit Hs. Consider calling AddHs() +207: [14:17:52] Tautomer enumeration stopped at 292 tautomers: max transforms reached +128: [14:17:52] done +128: [14:17:52] ------------------------------------- +128: [14:17:52] Test GitHub Issue 258: Bad pattern fingerprint for query molecule +212: .[14:17:52] Tautomer enumeration stopped at 22 tautomers: canceled +212: Enumeration was canceled due to timeout (50 ms) +128: [14:17:52] done +128: [14:17:52] ------------------------------------- +128: [14:17:52] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. +128: [14:17:52] DEPRECATION WARNING: please use AtomPairGenerator +128: [14:17:52] DEPRECATION WARNING: please use AtomPairGenerator +128: [14:17:52] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:52] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:52] done +128: [14:17:52] ------------------------------------- +128: [14:17:52] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints +128: [14:17:52] done +128: [14:17:52] ------------------------------------- +128: [14:17:52] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 +128: [14:17:52] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:52] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:52] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:52] done +128: [14:17:52] ------------------------------------- +128: [14:17:52] Test unfolded version of RDKFP +128: [14:17:52] ------------------------------------- +128: [14:17:52] Test bitinfo of RDKFP 128: 562: [ 2 ], 128: 709: [ 0 1 ], 128: 1118: [ 0 1 2 ], @@ -32154,100 +32185,1161 @@ 128: 1772: [ 0 ], [ 1 ], 128: 1813: [ 0 1 ], 128: ------------ -128: [17:55:27] ------------------------------------- -128: [17:55:27] Single atoms setting radius 1 bits in Morgan fingerprints -128: [17:55:27] done -128: [17:55:27] ------------------------------------- -128: [17:55:27] Github #879: Pattern fingerprint should set bits for single-atom fragments. -128: [17:55:27] done -128: [17:55:27] ------------------------------------- -128: [17:55:27] Github #1496: Pattern fingerprint setting bad bits for degree zero atoms -128: [17:55:27] done -128: [17:55:27] ------------------------------------- -128: [17:55:27] Github #1793: Fingerprint segfaults with branchedPaths=False and useHs=False -128: [17:55:27] done -128: [17:55:27] ------------------------------------- -128: [17:55:27] Github #1993: fingerprinters that use R/S labels should force a call to assignStereochemistry() if it hasn't already been called -128: [17:55:27] DEPRECATION WARNING: please use AtomPairGenerator -128: [17:55:27] DEPRECATION WARNING: please use AtomPairGenerator -128: [17:55:27] DEPRECATION WARNING: please use AtomPairGenerator -128: [17:55:27] DEPRECATION WARNING: please use AtomPairGenerator -128: [17:55:27] DEPRECATION WARNING: please use AtomPairGenerator -128: [17:55:27] DEPRECATION WARNING: please use AtomPairGenerator -128: [17:55:27] DEPRECATION WARNING: please use AtomPairGenerator -128: [17:55:27] DEPRECATION WARNING: please use AtomPairGenerator -128: [17:55:27] DEPRECATION WARNING: please use AtomPairGenerator -128: [17:55:27] DEPRECATION WARNING: please use AtomPairGenerator -128: [17:55:27] DEPRECATION WARNING: please use AtomPairGenerator -128: [17:55:27] DEPRECATION WARNING: please use AtomPairGenerator -128: [17:55:27] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:27] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:27] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:27] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:27] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:27] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:27] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:27] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:27] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:27] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:27] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:27] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [17:55:27] done -128: [17:55:27] ------------------------------------- -128: [17:55:27] Github #2115: BitInfo not complete for RDKFingerprint -128: [17:55:27] done -128: [17:55:27] ------------------------------------- -128: [17:55:27] Github #3723: Fingerprint crash for mols with Zero order bonds -128: [17:55:27] done -204/236 Test #128: testFingerprints ....................... Passed 7.11 sec -164: ........................................[17:55:27] The provided InitialSeed is not an MCS and will be ignored -164: [17:55:27] The provided InitialSeed is not an MCS and will be ignored -164: [17:55:27] The provided InitialSeed is not an MCS and will be ignored -164: .[17:55:27] The provided InitialSeed is not an MCS and will be ignored -164: [17:55:27] The provided InitialSeed is not an MCS and will be ignored -164: [17:55:27] The provided InitialSeed is not an MCS and will be ignored -164: .[17:55:27] The provided InitialSeed is not an MCS and will be ignored -164: [17:55:27] The provided InitialSeed is not an MCS and will be ignored -164: [17:55:27] The provided InitialSeed is not an MCS and will be ignored -164: .[17:55:27] The provided InitialSeed is not an MCS and will be ignored -164: [17:55:27] The provided InitialSeed is not an MCS and will be ignored -164: [17:55:27] The provided InitialSeed is not an MCS and will be ignored -164: ................. -164: ---------------------------------------------------------------------- -164: Ran 60 tests in 6.158s -164: -164: OK -195: ....................[17:55:27] Explicit valence for atom # 1 F, 2, is greater than permitted -195: [17:55:27] Explicit valence for atom # 6 F, 2, is greater than permitted -195: [17:55:27] Can't kekulize mol. Unkekulized atoms: 3 4 5 -205/236 Test #164: pyFMCS ................................. Passed 6.86 sec -207: [17:55:27] Tautomer enumeration stopped at 35 tautomers: canceled +128: [14:17:52] ------------------------------------- +128: [14:17:52] Single atoms setting radius 1 bits in Morgan fingerprints +128: [14:17:52] done +128: [14:17:52] ------------------------------------- +128: [14:17:52] Github #879: Pattern fingerprint should set bits for single-atom fragments. +128: [14:17:52] done +128: [14:17:52] ------------------------------------- +128: [14:17:52] Github #1496: Pattern fingerprint setting bad bits for degree zero atoms +128: [14:17:52] done +128: [14:17:52] ------------------------------------- +128: [14:17:52] Github #1793: Fingerprint segfaults with branchedPaths=False and useHs=False +128: [14:17:52] done +128: [14:17:52] ------------------------------------- +128: [14:17:52] Github #1993: fingerprinters that use R/S labels should force a call to assignStereochemistry() if it hasn't already been called +128: [14:17:52] DEPRECATION WARNING: please use AtomPairGenerator +128: [14:17:52] DEPRECATION WARNING: please use AtomPairGenerator +128: [14:17:52] DEPRECATION WARNING: please use AtomPairGenerator +128: [14:17:52] DEPRECATION WARNING: please use AtomPairGenerator +128: [14:17:52] DEPRECATION WARNING: please use AtomPairGenerator +128: [14:17:52] DEPRECATION WARNING: please use AtomPairGenerator +128: [14:17:52] DEPRECATION WARNING: please use AtomPairGenerator +128: [14:17:52] DEPRECATION WARNING: please use AtomPairGenerator +128: [14:17:52] DEPRECATION WARNING: please use AtomPairGenerator +128: [14:17:52] DEPRECATION WARNING: please use AtomPairGenerator +128: [14:17:52] DEPRECATION WARNING: please use AtomPairGenerator +128: [14:17:52] DEPRECATION WARNING: please use AtomPairGenerator +128: [14:17:52] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:52] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:52] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:52] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:52] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:52] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:52] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:52] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:52] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:52] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:52] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:52] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [14:17:52] done +128: [14:17:52] ------------------------------------- +128: [14:17:52] Github #2115: BitInfo not complete for RDKFingerprint +128: [14:17:52] done +128: [14:17:52] ------------------------------------- +128: [14:17:52] Github #3723: Fingerprint crash for mols with Zero order bonds +128: [14:17:52] done +203/236 Test #128: testFingerprints ....................... Passed 12.92 sec +207: [14:17:52] Tautomer enumeration stopped at 50 tautomers: max tautomers reached +204/236 Test #203: molStandardizeTest ..................... Passed 4.64 sec +148: [14:17:52] Molecule does not have explicit Hs. Consider calling AddHs() +232: ....... +232: ---------------------------------------------------------------------- +232: Ran 11 tests in 1.861s +232: +232: OK +205/236 Test #232: pySimDivPickers ........................ Passed 2.36 sec +146: validating reference data +186: [14:17:53] Relabelling existing label +170: Randomness seeded to: 937676665 +170: [14:17:53] Timed out after 11 seconds. +171: Randomness seeded to: 1237595372 +171: /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/data/chembl_1907596.smi +207: [14:17:53] Tautomer enumeration stopped at 18 tautomers: canceled 207: Enumeration was canceled due to timeout (50 ms) -195: .................[17:55:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -150: processing -150: launch :0 -150: launch :1 -150: launch :2 -150: launch :3 -186: bulk -173: [17:55:27] Building the fingerprints may take some time. +173: [14:17:53] Building the fingerprints may take some time. 236: ============================= test session starts ============================== 236: platform linux -- Python 3.13.5, pytest-8.3.5, pluggy-1.5.0 236: rootdir: /build/reproducible-path/rdkit-202503.1/Projects 236: configfile: pytest.ini 236: collected 12 items 236: -146: processing -146: launch :0 -146: launch :1 -146: launch :2 -146: launch :3 -232: ....... -232: ---------------------------------------------------------------------- -232: Ran 11 tests in 2.838s -232: -232: OK -206/236 Test #232: pySimDivPickers ........................ Passed 3.11 sec +74: [14:17:54] Finished: testSmiCorrectness() +74: [14:17:54] ----------------------------------------- +74: +74: [14:17:54] +74: ----------------------------------------- +74: [14:17:54] Spurious data before the first property will be ignored +74: [14:17:54] Property will be truncated after the first blank line +74: [14:17:54] Property will be truncated after the first blank line +74: [14:17:54] Property will be truncated after the first blank line +186: Best mapping +163: [14:17:54] The provided InitialSeed is not an MCS and will be ignored +222: Randomness seeded to: 1771702859 +222: =============================================================================== +222: All tests passed (203 assertions in 1 test case) +222: +206/236 Test #222: testMolProcessing ...................... Passed 5.56 sec +74: [14:17:55] Finished: testSDCorrectness() +74: [14:17:55] ----------------------------------------- +74: +207/236 Test #74: testMultithreadedMolSupplier ........... Passed 17.51 sec +208/236 Test #186: testRGroupDecomp ....................... Passed 10.06 sec +183: [14:17:55] ------------------------------------- +183: [14:17:55] testing PatternHolder +195: ....................[14:17:55] Explicit valence for atom # 1 F, 2, is greater than permitted +195: [14:17:55] Explicit valence for atom # 6 F, 2, is greater than permitted +195: [14:17:55] Can't kekulize mol. Unkekulized atoms: 3 4 5 +148: .[14:17:55] Molecule does not have explicit Hs. Consider calling AddHs() +173: [14:17:55] +173: +173: **** +173: Invariant Violation +173: molzip: bond info not properly setup for bgn atom with label:1 +173: Violation occurred on line 1090 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp +173: Failed Expression: bond.a +173: ---------- +173: Stacktrace: +173: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +173: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +173: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 +173: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 +173: 4# RDKit::molzip(RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 +173: 5# RDKit::SynthonSpaceSearch::SynthonSet::makeSynthonSearchMols() in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSynthonSpaceSearch.so.1 +173: 6# RDKit::SynthonSpaceSearch::SynthonSpace::readTextFile(std::__cxx11::basic_string, std::allocator > const&, bool&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSynthonSpaceSearch.so.1 +173: 7# 0x0000560FB478156A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: 8# 0x0000560FB47CBD78 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: 9# 0x0000560FB47CC898 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: 10# 0x0000560FB47CCD10 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: 11# 0x0000560FB479E2C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: 12# 0x0000560FB479E62C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: 13# 0x0000560FB478078E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: 14# 0x00007FDD83E33CA8 in /lib/x86_64-linux-gnu/libc.so.6 +173: 15# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +173: 16# 0x0000560FB47807D1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: ---------- +173: **** +173: +173: [14:17:55] Error:: in reaction amide-1 :: building molecule from synthons : 1-1 (c1cc[1*]ccc1C(=O)[1*]) and 2-1 ([1*]N1CCCC1) +173: molzip: bond info not properly setup for bgn atom with label:1 +173: [14:17:55] Explicit valence for atom # 4 C, 5, is greater than permitted +173: [14:17:55] Error:: in reaction error-1 :: building molecule from synthons : 1-1 (C(=[2*])=CC=[1*]) and 2-1 (ClC([2*])=CN=[1*]) +173: Explicit valence for atom # 4 C, 5, is greater than permitted +173: [14:17:55] Complex queries can be slow. +195: .................[14:17:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +212: Enumeration has completed +183: [14:17:55] ------------------------------------- +183: [14:17:55] testing TautomerPatternHolder +212: [14:17:55] Tautomer enumeration stopped at 33 tautomers: canceled +173: [14:17:56] Complex queries can be slow. +29: Checking against /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +183: [14:17:56] ------------------------------------- +183: [14:17:56] testSegFaultInHolder +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1[14:17:56] [14:17:56] [14:17:56] [14:17:56] SMILES Parse Error: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1:[14:17:56] :SMILES Parse Error: +183: syntax errorSMILES Parse Error: [14:17:56] syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] Failed parsing SMILES 'dsafsdf'dsafsdf[14:17:56] SMILES Parse Error: syntax error while parsing: +183: while parsing: for input: 'dsafsdf' +183: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: syntax errordsafsdf while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1:[14:17:56] [14:17:56] [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: dsafsdf +183: : +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] +183: [14:17:56] [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: '[14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdfdsafsdf' +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdfdsafsdf[14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^SMILES Parse Error: syntax error while parsing: +183: [14:17:56] ^ +183: +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: ' +183: +183: [14:17:56] ^ +183: [14:17:56] SMILES[14:17:56] SMILES Parse Error: [14:17:56] syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: SMILES[14:17:56] [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf[14:17:56] +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf[14:17:56] SMILES Parse Error: [14:17:56] SMILES Parse Error: SMILESSMILES Parse Error: syntax error while parsing: dsafsdf Parse Error: syntax errordsafsdf while parsing: dsafsdf +183: +183: [14:17:56] [14:17:56] [14:17:56] SMILES Parse Error: syntax errorSMILES Parse Error: check for mistakes around position 1: +183: while parsing: dsafsdf[14:17:56] SMILES Parse Error: check for mistakes around position 1[14:17:56] [14:17:56] dsafsdf +183: [14:17:56] ^ +183: +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] SMILES Parse Error: SMILES Parse Error: :[14:17:56] [14:17:56] dsafsdf +183: SMILES Parse Error: syntax error while parsing: dsafsdf +183: +183: [14:17:56] SMILES Parse Error: check for mistakes around position [14:17:56] +183: [14:17:56] Failed parsing SMILES 'dsafsdf'SMILES Parse Error: check for mistakes around position 1[14:17:56] 1^: +183: syntax error[14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax errorSMILES Parse Error: while parsing: dsafsdf +183: while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf'syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: for input: 'dsafsdf' +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] +183: SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] SMILES[14:17:56] Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] [14:17:56] SMILES Parse Error: dsafsdf +183: [14:17:56] ^ +183: 1: +183: [14:17:56] dsafsdf[14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: SMILES Parse Error: : +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] [14:17:56] dsafsdf +183: syntax error while parsing: dsafsdf +183: +183: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position [14:17:56] [14:17:56] SMILES Parse Error: syntax error1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^[14:17:56] +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf[14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf[14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: syntax error[14:17:56] [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] SMILES Parse Error: [14:17:56] Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: syntax error[14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [14:17:56] SMILES Parse Error: check for mistakes around position 1: +183: [14:17:56] dsafsdf +183: [14:17:56] ^ +183: [14:17:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [14:17:56] ------------------------------------- +183: [14:17:56] Results do not depend on numThreads +212: ..........[14:17:56] Explicit valence for atom # 1 N, 4, is greater than permitted +212: [14:17:56] Explicit valence for atom # 1 N, 4, is greater than permitted +212: [14:17:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +212: [14:17:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +173: [14:17:56] Complex queries can be slow. +29: All 191 tests passed +173: [14:17:57] Complex queries can be slow. +29: +29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_dative.smi... +207: 375 +207: Enumeration has completed +207: [14:17:57] Tautomer enumeration stopped at 21 tautomers: canceled 126: Warning: Atom Count for residue GLU5A does not match expected count 126: Warning: Atom Count for residue ASN39A does not match expected count 126: Warning: Atom Count for residue GLU53A does not match expected count @@ -32255,58 +33347,58 @@ 126: Warning: Atom Count for residue LYS80A does not match expected count 126: Warning: Atom Count for residue GLU150A does not match expected count 126: Warning: Atom Count for residue ASN157A does not match expected count -126: .[17:55:28] DEPRECATION WARNING: please use MorganGenerator -126: .[17:55:28] DEPRECATION WARNING: please use MorganGenerator -126: ..[17:55:28] DEPRECATION WARNING: please use AtomPairGenerator -126: [17:55:28] DEPRECATION WARNING: please use AtomPairGenerator -126: [17:55:28] DEPRECATION WARNING: please use AtomPairGenerator -126: [17:55:28] DEPRECATION WARNING: please use AtomPairGenerator -126: [17:55:28] DEPRECATION WARNING: please use AtomPairGenerator -126: [17:55:28] DEPRECATION WARNING: please use AtomPairGenerator -126: .[17:55:28] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [17:55:28] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: ...[17:55:28] DEPRECATION WARNING: please use MorganGenerator -126: [17:55:28] DEPRECATION WARNING: please use MorganGenerator -126: [17:55:28] DEPRECATION WARNING: please use MorganGenerator -126: [17:55:28] DEPRECATION WARNING: please use MorganGenerator -126: [17:55:28] DEPRECATION WARNING: please use MorganGenerator -126: [17:55:28] DEPRECATION WARNING: please use MorganGenerator -126: [17:55:28] DEPRECATION WARNING: please use MorganGenerator -126: [17:55:28] DEPRECATION WARNING: please use MorganGenerator -126: [17:55:28] DEPRECATION WARNING: please use MorganGenerator -126: [17:55:28] DEPRECATION WARNING: please use MorganGenerator -126: [17:55:28] DEPRECATION WARNING: please use MorganGenerator -126: [17:55:28] DEPRECATION WARNING: please use MorganGenerator -126: [17:55:28] DEPRECATION WARNING: please use MorganGenerator -126: [17:55:28] DEPRECATION WARNING: please use MorganGenerator -126: [17:55:28] DEPRECATION WARNING: please use MorganGenerator -126: [17:55:28] DEPRECATION WARNING: please use MorganGenerator -126: [17:55:28] DEPRECATION WARNING: please use MorganGenerator -126: [17:55:28] DEPRECATION WARNING: please use MorganGenerator -126: [17:55:28] DEPRECATION WARNING: please use MorganGenerator -126: [17:55:28] DEPRECATION WARNING: please use MorganGenerator -126: [17:55:28] DEPRECATION WARNING: please use MorganGenerator -126: [17:55:28] DEPRECATION WARNING: please use MorganGenerator -126: ....[17:55:28] DEPRECATION WARNING: please use AtomPairGenerator -126: [17:55:28] DEPRECATION WARNING: please use AtomPairGenerator -126: ....[17:55:28] DEPRECATION WARNING: please use AtomPairGenerator -126: [17:55:28] DEPRECATION WARNING: please use AtomPairGenerator -126: .[17:55:28] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [17:55:28] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [17:55:28] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [17:55:28] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [17:55:28] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: ..[17:55:28] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [17:55:28] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [17:55:28] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [17:55:28] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [17:55:28] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [17:55:28] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: .[17:55:28] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [17:55:28] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: .[14:17:57] DEPRECATION WARNING: please use MorganGenerator +126: .[14:17:57] DEPRECATION WARNING: please use MorganGenerator +126: ..[14:17:57] DEPRECATION WARNING: please use AtomPairGenerator +126: [14:17:57] DEPRECATION WARNING: please use AtomPairGenerator +126: [14:17:57] DEPRECATION WARNING: please use AtomPairGenerator +126: [14:17:57] DEPRECATION WARNING: please use AtomPairGenerator +126: [14:17:57] DEPRECATION WARNING: please use AtomPairGenerator +126: [14:17:57] DEPRECATION WARNING: please use AtomPairGenerator +126: .[14:17:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [14:17:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: ...[14:17:57] DEPRECATION WARNING: please use MorganGenerator +126: [14:17:57] DEPRECATION WARNING: please use MorganGenerator +126: [14:17:57] DEPRECATION WARNING: please use MorganGenerator +126: [14:17:57] DEPRECATION WARNING: please use MorganGenerator +126: [14:17:57] DEPRECATION WARNING: please use MorganGenerator +126: [14:17:57] DEPRECATION WARNING: please use MorganGenerator +126: [14:17:57] DEPRECATION WARNING: please use MorganGenerator +126: [14:17:57] DEPRECATION WARNING: please use MorganGenerator +126: [14:17:57] DEPRECATION WARNING: please use MorganGenerator +126: [14:17:57] DEPRECATION WARNING: please use MorganGenerator +126: [14:17:57] DEPRECATION WARNING: please use MorganGenerator +126: [14:17:57] DEPRECATION WARNING: please use MorganGenerator +126: [14:17:57] DEPRECATION WARNING: please use MorganGenerator +126: [14:17:57] DEPRECATION WARNING: please use MorganGenerator +126: [14:17:57] DEPRECATION WARNING: please use MorganGenerator +126: [14:17:57] DEPRECATION WARNING: please use MorganGenerator +126: [14:17:57] DEPRECATION WARNING: please use MorganGenerator +126: [14:17:57] DEPRECATION WARNING: please use MorganGenerator +126: [14:17:57] DEPRECATION WARNING: please use MorganGenerator +126: [14:17:57] DEPRECATION WARNING: please use MorganGenerator +126: [14:17:57] DEPRECATION WARNING: please use MorganGenerator +126: [14:17:57] DEPRECATION WARNING: please use MorganGenerator +126: ....[14:17:57] DEPRECATION WARNING: please use AtomPairGenerator +126: [14:17:57] DEPRECATION WARNING: please use AtomPairGenerator +126: ....[14:17:57] DEPRECATION WARNING: please use AtomPairGenerator +126: [14:17:57] DEPRECATION WARNING: please use AtomPairGenerator +126: .[14:17:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [14:17:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [14:17:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [14:17:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [14:17:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: ..[14:17:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [14:17:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [14:17:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [14:17:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [14:17:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [14:17:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: .[14:17:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [14:17:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: ... 126: ---------------------------------------------------------------------- -126: Ran 31 tests in 7.924s +126: Ran 31 tests in 16.820s 126: 126: OK 126: exactmw 78.046950192 @@ -32355,70 +33447,40 @@ 126: CustomNumAtoms 6.0 126: exactmw 78.046950192 126: lipinskiHBA 0.0 -207: 375 -207: Enumeration has completed -207/236 Test #126: pyMolDescriptors ....................... Passed 8.45 sec -212: Enumeration has completed -207: [17:55:28] Tautomer enumeration stopped at 59 tautomers: canceled -212: [17:55:28] Tautomer enumeration stopped at 60 tautomers: canceled -222: Randomness seeded to: 4156691398 -222: =============================================================================== -222: All tests passed (203 assertions in 1 test case) -222: -173: [17:55:28] -173: -173: **** -173: Invariant Violation -173: molzip: bond info not properly setup for bgn atom with label:1 -173: Violation occurred on line 1090 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp -173: Failed Expression: bond.a -173: ---------- -173: Stacktrace: -173: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -173: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -173: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 -173: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 -173: 4# RDKit::molzip(RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 -173: 5# RDKit::SynthonSpaceSearch::SynthonSet::makeSynthonSearchMols() in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSynthonSpaceSearch.so.1 -173: 6# RDKit::SynthonSpaceSearch::SynthonSpace::readTextFile(std::__cxx11::basic_string, std::allocator > const&, bool&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSynthonSpaceSearch.so.1 -173: 7# 0x000055B2CCA5556A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: 8# 0x000055B2CCA9FD78 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: 9# 0x000055B2CCAA0898 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: 10# 0x000055B2CCAA0D10 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: 11# 0x000055B2CCA722C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: 12# 0x000055B2CCA7262C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: 13# 0x000055B2CCA5478E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: 14# 0x00007F21B1233CA8 in /lib/x86_64-linux-gnu/libc.so.6 -173: 15# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -173: 16# 0x000055B2CCA547D1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: ---------- -173: **** -173: -173: [17:55:28] Error:: in reaction amide-1 :: building molecule from synthons : 1-1 (c1cc[1*]ccc1C(=O)[1*]) and 2-1 ([1*]N1CCCC1) -173: molzip: bond info not properly setup for bgn atom with label:1 -173: [17:55:28] Explicit valence for atom # 4 C, 5, is greater than permitted -173: [17:55:28] Error:: in reaction error-1 :: building molecule from synthons : 1-1 (C(=[2*])=CC=[1*]) and 2-1 (ClC([2*])=CN=[1*]) -173: Explicit valence for atom # 4 C, 5, is greater than permitted -173: [17:55:28] Complex queries can be slow. -208/236 Test #222: testMolProcessing ...................... Passed 3.95 sec -212: ..........[17:55:28] Explicit valence for atom # 1 N, 4, is greater than permitted -212: [17:55:28] Explicit valence for atom # 1 N, 4, is greater than permitted -212: [17:55:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -212: [17:55:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -173: [17:55:28] Complex queries can be slow. -173: [17:55:29] Complex queries can be slow. -173: [17:55:29] Complex queries can be slow. -173: [17:55:29] Complex queries can be slow. -125: Warning: Atom Count for residue GLU5A does not match expected count -125: Warning: Atom Count for residue ASN39A does not match expected count -125: Warning: Atom Count for residue GLU53A does not match expected count -125: Warning: Atom Count for residue ARG64A does not match expected count -125: Warning: Atom Count for residue LYS80A does not match expected count -125: Warning: Atom Count for residue GLU150A does not match expected count -125: Warning: Atom Count for residue ASN157A does not match expected count -183: [17:55:29] ------------------------------------- -183: [17:55:29] testing PatternHolder -173: [17:55:29] Complex queries can be slow. +209/236 Test #126: pyMolDescriptors ....................... Passed 18.41 sec +173: [14:17:57] Complex queries can be slow. +164: ........................................[14:17:58] The provided InitialSeed is not an MCS and will be ignored +164: [14:17:58] The provided InitialSeed is not an MCS and will be ignored +164: [14:17:58] The provided InitialSeed is not an MCS and will be ignored +173: [14:17:58] Complex queries can be slow. +164: .[14:17:58] The provided InitialSeed is not an MCS and will be ignored +164: [14:17:58] The provided InitialSeed is not an MCS and will be ignored +164: [14:17:58] The provided InitialSeed is not an MCS and will be ignored +164: .[14:17:58] The provided InitialSeed is not an MCS and will be ignored +164: [14:17:58] The provided InitialSeed is not an MCS and will be ignored +164: [14:17:58] The provided InitialSeed is not an MCS and will be ignored +164: .[14:17:58] The provided InitialSeed is not an MCS and will be ignored +164: [14:17:58] The provided InitialSeed is not an MCS and will be ignored +164: [14:17:58] The provided InitialSeed is not an MCS and will be ignored +164: ................. +164: ---------------------------------------------------------------------- +164: Ran 60 tests in 16.432s +164: +164: OK +210/236 Test #164: pyFMCS ................................. Passed 17.31 sec +212: ............[14:17:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +212: [14:17:59] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 1 ignored. +212: [14:17:59] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 1 ignored. +173: [14:17:59] Complex queries can be slow. +212: ........[14:17:59] Explicit valence for atom # 1 O, 3, is greater than permitted +212: .. +212: ---------------------------------------------------------------------- +212: Ran 38 tests in 10.265s +212: +212: OK +212: done +211/236 Test #212: pyMolStandardize ....................... Passed 11.59 sec +173: [14:18:00] Complex queries can be slow. 207: CN=c1cc[nH]cn1 207: CN=c1ccnc[nH]1 207: CNc1ccncn1 @@ -32426,1056 +33488,24 @@ 207: CN=c1cccc[nH]1 207: CNc1ccccn1 207: res: CNc1ccccn1 -125: =============================================================================== -125: All tests passed (515 assertions in 10 test cases) -125: -209/236 Test #125: descriptorsTestCatch ................... Passed 9.64 sec -173: [17:55:29] Complex queries can be slow. -173: [17:55:29] Complex queries can be slow. -183: [17:55:29] ------------------------------------- -183: [17:55:29] testing TautomerPatternHolder -210/236 Test #207: molTautomerTest ........................ Passed 6.06 sec -74: [17:55:29] Finished: testSmiCorrectness() -74: [17:55:29] ----------------------------------------- -74: -74: [17:55:29] -74: ----------------------------------------- -74: [17:55:30] Spurious data before the first property will be ignored -74: [17:55:30] Property will be truncated after the first blank line -74: [17:55:30] Property will be truncated after the first blank line -74: [17:55:30] Property will be truncated after the first blank line -173: [17:55:30] Complex queries can be slow. -183: [17:55:30] ------------------------------------- -183: [17:55:30] testSegFaultInHolder -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf[17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf[17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: ' -183: ' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] [17:55:30] [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf[17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: -183: ^[17:55:30] ^ -183: -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: '[17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] [17:55:30] [17:55:30] [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] [17:55:30] [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf[17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'[17:55:30] SMILES Parse Error: syntax error while parsing: [17:55:30] [17:55:30] [17:55:30] [17:55:30] SMILES Parse Error: [17:55:30] [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: SMILES Parse Error: [17:55:30] syntax error while parsing: dsafsdfdsafsdf[17:55:30] SMILES Parse Error: -183: -183: [17:55:30] [17:55:30] dsafsdfSMILES Parse Error: check for mistakes around position 1:[17:55:30] [17:55:30] SMILES Parse Error: [17:55:30] [17:55:30] SMILES Parse Error: syntax error while parsing: SMILES Parse Error: SMILES Parse Error: [17:55:30] [17:55:30] ^ -183: -183: SMILES Parse Error: syntax error -183: SMILES Parse Error: SMILES Parse Error: syntax errorSMILES Parse Error: syntax errorsyntax error -183: while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: SMILES Parse Error: SMILES Parse Error: syntax errorsyntax error while parsing: dsafsdf -183: while parsing: [17:55:30] dsafsdf -183: SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] [17:55:30] SMILES Parse Error: syntax errorsyntax error while parsing: dsafsdf[17:55:30] [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position [17:55:30] -183: [17:55:30] dsafsdf -183: SMILES Parse Error: syntax error[17:55:30] syntax error while parsing: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: SMILES Parse Error: check for mistakes around position while parsing: dsafsdf -183: [17:55:30] syntax error while parsing: dsafsdf -183: [17:55:30] [17:55:30] SMILES Parse Error: check for mistakes around position 1:SMILES Parse Error: check for mistakes around position -183: [17:55:30] dsafsdfsyntax errorSMILES Parse Error: check for mistakes around position -183: SMILES Parse Error: check for mistakes around position 11: -183: SMILES Parse Error: while parsing: syntax error while parsing: [17:55:30] dsafsdfSMILES Parse Error: check for mistakes around position -183: 1[17:55:30] [17:55:30] 1^: -183: while parsing: while parsing: SMILES Parse Error: while parsing: [17:55:30] dsafsdf1SMILES Parse Error: : -183: dsafsdf[17:55:30] -183: :dsafsdf -183: dsafsdf -183: syntax error while parsing: SMILES Parse Error: check for mistakes around position dsafsdf1 -183: : -183: dsafsdf[17:55:30] SMILES Parse Error: check for mistakes around position [17:55:30] :dsafsdf1 -183: : -183: -183: dsafsdf[17:55:30] [17:55:30] [17:55:30] -183: SMILES Parse Error: check for mistakes around position -183: dsafsdf[17:55:30] [17:55:30] SMILESSMILES Parse Error: check for mistakes around position ^ Parse Error: dsafsdfsyntax error[17:55:30] -183: 1[17:55:30] [17:55:30] : -183: -183: ^dsafsdf -183: [17:55:30] -183: [17:55:30] [17:55:30] SMILES Parse Error: check for mistakes around position [17:55:30] -183: [17:55:30] while parsing: [17:55:30] [17:55:30] 1 -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: -183: -183: Failed parsing SMILES 'dsafsdf' for input: '1[17:55:30] dsafsdf:[17:55:30] -183: SMILES Parse Error: check for mistakes around position dsafsdf -183: SMILES Parse Error: check for mistakes around position SMILES Parse Error: check for mistakes around position SMILES Parse Error: check for mistakes around position ^dsafsdf -183: 1^ -183: [17:55:30] :[17:55:30] -183: dsafsdf -183: :'SMILES11: -183: -183: -183: [17:55:30] [17:55:30] [17:55:30] ^^ -183: -183: Parse Error: [17:55:30] Failed parsing SMILES 'dsafsdf'[17:55:30] 1SMILESSMILES Parse Error: check for mistakes around position : -183: Parse Error: Failed parsing SMILES 'dsafsdf' -183: [17:55:30] [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: '[17:55:30] dsafsdf' -183: SMILESdsafsdf Parse Error: [17:55:30] 1: for input: '[17:55:30] SMILES for input: 'dsafsdf'dsafsdf[17:55:30] dsafsdf: -183: -183: [17:55:30] -183: [17:55:30] [17:55:30] Parse Error: SMILESSMILES Parse Error: check for mistakes around position [17:55:30] -183: SMILES Parse Error: dsafsdf^Failed parsing SMILES 'dsafsdf' -183: for input: 'dsafsdfdsafsdf -183: [17:55:30] ^Failed parsing SMILES 'dsafsdf'dsafsdf for input: 'dsafsdf -183: -183: [17:55:30] Parse Error: -183: [17:55:30] dsafsdf' -183: 'Failed parsing SMILES 'dsafsdf'[17:55:30] for input: 'dsafsdf -183: -183: 1:Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'[17:55:30] dsafsdf[17:55:30] -183: ^ -183: 1 -183: ^[17:55:30] -183: ' -183: [17:55:30] [17:55:30] '^SMILES -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: -183: -183: [17:55:30] Parse Error: Failed parsing SMILES 'dsafsdf'^dsafsdf[17:55:30] -183: :^ -183: -183: dsafsdf[17:55:30] [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: ^^ -183: -183: [17:55:30] -183: -183: ^dsafsdf[17:55:30] -183: ^ -183: SMILES -183: Parse Error: [17:55:30] -183: for input: '[17:55:30] -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: [17:55:30] dsafsdf -183: [17:55:30] Failed parsing SMILES 'dsafsdf'SMILES for input: 'Failed parsing SMILES 'dsafsdf'[17:55:30] [17:55:30] [17:55:30] dsafsdfdsafsdf Parse Error: [17:55:30] Failed parsing SMILES 'dsafsdf'[17:55:30] 'SMILES -183: ^ -183: SMILES Parse Error: ' -183: for input: ' for input: '[17:55:30] dsafsdf'^SMILES -183: SMILES -183: ^[17:55:30] -183: dsafsdfSMILES -183: [17:55:30] dsafsdfSMILES Parse Error: ' -183: Parse Error: Parse Error: Failed parsing SMILES 'dsafsdf' Parse Error: for input: 'Failed parsing SMILES 'dsafsdf'Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf for input: 'dsafsdf' Parse Error: dsafsdf''[17:55:30] -183: SMILESFailed parsing SMILES 'dsafsdf' Parse Error: Failed parsing SMILES 'dsafsdf' -183: for input: 'dsafsdf -183: [17:55:30] Failed parsing SMILES 'dsafsdf'^ for input: '' for input: ' -183: dsafsdf'dsafsdf -183: ' -183: -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] [17:55:30] [17:55:30] [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1:[17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] [17:55:30] [17:55:30] SMILES Parse Error: syntax error while parsing: [17:55:30] [17:55:30] SMILES Parse Error: [17:55:30] [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: -183: SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position SMILES Parse Error: SMILES Parse Error: [17:55:30] [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] [17:55:30] SMILES Parse Error: syntax errorSMILES Parse Error: [17:55:30] [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: syntax error while parsing: dsafsdf -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'[17:55:30] -183: SMILES Parse Error: [17:55:30] SMILES Parse Error: check for mistakes around position dsafsdf -183: syntax error[17:55:30] [17:55:30] 1: -183: [17:55:30] SMILES Parse Error: syntax errorSMILES Parse Error: [17:55:30] syntax errorSMILES Parse Error: syntax error while parsing: 1SMILES Parse Error: syntax error[17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: syntax error[17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: : -183: syntax error[17:55:30] ^SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: while parsing: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: SMILES Parse Error: [17:55:30] syntax error while parsing: dsafsdf -183: while parsing: [17:55:30] while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position while parsing: 1: -183: syntax errordsafsdf while parsing: -183: SMILES Parse Error: check for mistakes around position SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf while parsing: SMILES Parse Error: syntax error while parsing: dsafsdfdsafsdf -183: [17:55:30] -183: dsafsdfdsafsdf -183: 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: [17:55:30] syntax error while parsing: dsafsdf -183: [17:55:30] SMILES[17:55:30] -183: [17:55:30] ^[17:55:30] SMILES Parse Error: syntax errordsafsdf[17:55:30] -183: SMILES Parse Error: Failed parsing SMILES 'dsafsdf'[17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] [17:55:30] SMILES Parse Error: syntax error while parsing: [17:55:30] dsafsdfSMILES Parse Error: SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] [17:55:30] ^ -183: SMILES Parse Error: syntax error while parsing: SMILES Parse Error: Parse Error: syntax error[17:55:30] SMILES Parse Error: SMILESsyntax error while parsing: [17:55:30] SMILES Parse Error: [17:55:30] dsafsdfsyntax errordsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] SMILES Parse Error: check for mistakes around position dsafsdf -183: -183: -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1:[17:55:30] [17:55:30] SMILES Parse Error: [17:55:30] ^ -183: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf for input: 'dsafsdf' -183: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1 while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1:syntax error -183: while parsing: dsafsdf -183: [17:55:30] [17:55:30] while parsing: -183: [17:55:30] 1dsafsdfsyntax error1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: Parse Error: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: dsafsdf -183: [17:55:30] SMILES Parse Error: : -183: [17:55:30] ^ -183: : -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf'[17:55:30] [17:55:30] [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position ' while parsing: [17:55:30] while parsing: SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] [17:55:30] SMILES Parse Error: SMILESsyntax error while parsing: SMILES Parse Error: check for mistakes around position dsafsdfSMILES Parse Error: -183: 1 -183: -183: 1: -183: SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] dsafsdf -183: SMILES Parse Error: check for mistakes around position [17:55:30] [17:55:30] Failed parsing SMILES 'dsafsdf' while parsing: Parse Error: [17:55:30] dsafsdf^Failed parsing SMILES 'dsafsdf' for input: 'dsafsdfdsafsdfSMILES Parse Error: check for mistakes around position dsafsdf[17:55:30] syntax errorSMILES Parse Error: [17:55:30] [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1:SMILES Parse Error: check for mistakes around position -183: [17:55:30] [17:55:30] SMILES Parse Error: check for mistakes around position dsafsdf1 for input: 'dsafsdf' -183: 1 -183: [17:55:30] dsafsdf -183: :[17:55:30] -183: [17:55:30] [17:55:30] SMILES Parse Error: check for mistakes around position 1[17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] -183: [17:55:30] :SMILES Parse Error: check for mistakes around position 1:SMILES Parse Error: check for mistakes around position -183: 1[17:55:30] dsafsdf: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: SMILES Parse Error: Failed parsing SMILES 'dsafsdf'dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: -183: ^ -183: -183: -183: [17:55:30] dsafsdf -183: -183: [17:55:30] [17:55:30] [17:55:30] [17:55:30] dsafsdf -183: [17:55:30] ^ -183: :1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'[17:55:30] SMILES Parse Error: [17:55:30] SMILES Parse Error: check for mistakes around position SMILES1 Parse Error: SMILES Parse Error: check for mistakes around position 1 -183: dsafsdfdsafsdf -183: -183: [17:55:30] dsafsdf -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: : -183: [17:55:30] [17:55:30] SMILES Parse Error: [17:55:30] ::Failed parsing SMILES 'dsafsdf' -183: -183: [17:55:30] -183: ^Failed parsing SMILES 'dsafsdf'[17:55:30] for input: '^ -183: dsafsdf[17:55:30] [17:55:30] dsafsdf -183: for input: '[17:55:30] dsafsdf' -183: -183: [17:55:30] SMILES Parse Error: check for mistakes around position -183: Failed parsing SMILES 'dsafsdf'[17:55:30] dsafsdf -183: SMILES -183: [17:55:30] ^ -183: [17:55:30] 1SMILES[17:55:30] [17:55:30] SMILES[17:55:30] dsafsdf'dsafsdf[17:55:30] Parse Error: ^ -183: Failed parsing SMILES 'dsafsdf' for input: '[17:55:30] dsafsdf[17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf[17:55:30] ^ -183: -183: Parse Error: ^ -183: ^ -183: [17:55:30] :[17:55:30] SMILES -183: Parse Error: [17:55:30] Failed parsing SMILES 'dsafsdf'SMILES Parse Error: for input: ' -183: Failed parsing SMILES 'dsafsdf' for input: ' -183: [17:55:30] ^' Parse Error: syntax errorFailed parsing SMILES 'dsafsdf'SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: ^ -183: [17:55:30] for input: 'dsafsdfdsafsdf'[17:55:30] SMILES -183: -183: dsafsdfdsafsdf[17:55:30] '^ for input: 'dsafsdf for input: '' -183: while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: ' -183: ' -183: -183: -183: SMILES Parse Error: [17:55:30] dsafsdf -183: ' -183: -183: [17:55:30] ^ -183: [17:55:30] ^ -183: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] Parse Error: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdfFailed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: ' -183: [17:55:30] SMILES[17:55:30] SMILES Parse Error: dsafsdfFailed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' Parse Error: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] ^^ -183: for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: ' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [17:55:30] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [17:55:30] SMILES Parse Error: check for mistakes around position 1: -183: [17:55:30] dsafsdf -183: [17:55:30] ^ -183: [17:55:30] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -173: [17:55:30] Complex queries can be slow. -183: [17:55:30] ------------------------------------- -183: [17:55:30] Results do not depend on numThreads -173: [17:55:30] Complex queries can be slow. -74: [17:55:30] Finished: testSDCorrectness() -74: [17:55:30] ----------------------------------------- -74: -211/236 Test #74: testMultithreadedMolSupplier ........... Passed 11.10 sec -212: ............[17:55:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -212: [17:55:30] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 1 ignored. -212: [17:55:30] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 1 ignored. -186: bulk, no symmetry -29: Checking against /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -212: ........[17:55:30] Explicit valence for atom # 1 O, 3, is greater than permitted -29: All 191 tests passed -212: .. -212: ---------------------------------------------------------------------- -212: Ran 38 tests in 6.436s -212: -212: OK -212: done +80: =============================================================================== +80: All tests passed (1596 assertions in 100 test cases) +80: +212/236 Test #80: fileParsersCatchTest ................... Passed 22.74 sec +173: [14:18:00] Complex queries can be slow. +213/236 Test #207: molTautomerTest ........................ Passed 12.78 sec +146: processing +146: launch :0 +146: launch :1 +146: launch :2 +146: launch :3 +173: [14:18:01] Complex queries can be slow. +173: [14:18:03] Complex queries can be slow. 159: Done 159: ----------------- Test Github #781: Rendering single-atom molecules 159: Done 159: ----------------- Test 3 -212/236 Test #212: pyMolStandardize ....................... Passed 6.94 sec 159: file test3_1.png gave hash 123800385U not the expected 675908852U -29: -29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.smi... 159: file test3_2.png gave hash 1032419673U not the expected 2452584093U 159: file test3_3.png gave hash 4020047355U not the expected 1907006999U 159: file test3_4.png gave hash 3725504342U not the expected 2305641511U @@ -33541,7 +33571,6 @@ 159: ----------------- Testing github 1829: crash when drawMolecules() is called with an empty list 159: Done 159: ----------------- Testing use of fixed scales for drawing. -186: [17:55:31] Relabelling existing label 159: Done 159: ----------------- Testing rotation of 2D drawing. 159: Done @@ -33558,32 +33587,45 @@ 159: ----------------- Testing testGithub2931: multi-coloured molecule highlights. 159: file testGithub2931_1.svg gave hash 811930351U not the expected 3635831631U 159: file testGithub2931_3.svg gave hash 1986517899U not the expected 2885834646U +125: Warning: Atom Count for residue GLU5A does not match expected count +125: Warning: Atom Count for residue ASN39A does not match expected count +125: Warning: Atom Count for residue GLU53A does not match expected count +125: Warning: Atom Count for residue ARG64A does not match expected count +125: Warning: Atom Count for residue LYS80A does not match expected count +125: Warning: Atom Count for residue GLU150A does not match expected count +125: Warning: Atom Count for residue ASN157A does not match expected count +183: [14:18:05] ------------------------------------- +183: [14:18:05] Results do not depend on numThreads (all same) 159: Done 159: ----------------- Testing annotation of 2D Drawing. 159: file test20_1.png gave hash 1197378089U not the expected 200877868U 159: file test20_2.png gave hash 717262667U not the expected 1651164846U +125: =============================================================================== +125: All tests passed (515 assertions in 10 test cases) +125: +214/236 Test #125: descriptorsTestCatch ................... Passed 26.34 sec +183: [14:18:05] ------------------------------------- +183: [14:18:05] testTautomerQueries 159: file test20_3.png gave hash 1844565424U not the expected 1463603076U 159: file test20_4.png gave hash 284908271U not the expected 1714613205U +183: [14:18:05] Pattern fingerprints for tautomersearch aren't tautomer fingerprints, ignoring... +183: [14:18:05] ------------------------------------- +183: [14:18:05] github3881 recursive smarts with rings 159: Done 159: ----------------- Test 21 - different font +215/236 Test #183: substructLibraryTest ................... Passed 21.22 sec 159: Done 159: ----------------- Test 22 - draw explicit methyls. 159: Done 159: ----------------- Testing drawing of legends. -80: =============================================================================== -80: All tests passed (1596 assertions in 100 test cases) -80: 159: Done 159: ----------------- Test Github 3305 - change and scale line widths. -213/236 Test #80: fileParsersCatchTest ................... Passed 12.04 sec 159: file testGithub3305_1.png gave hash 3066881557U not the expected 3303791649U 159: file testGithub3305_2.png gave hash 3473051322U not the expected 4003267433U 159: file testGithub3305_3.png gave hash 748608900U not the expected 273338209U 159: file testGithub3305_4.png gave hash 3317652686U not the expected 3842605920U 159: file testGithub3305_5.png gave hash 2008868897U not the expected 151279576U -214/236 Test #199: pyTestThreads .......................... Passed 8.00 sec 159: file testGithub3305_5.svg gave hash 3310590632U not the expected 1335449325U -186: Best mapping 159: file testGithub3305_6.png gave hash 1479310253U not the expected 613418460U 159: file testGithub3305_7.png gave hash 526001191U not the expected 2835747678U 159: Done @@ -33597,495 +33639,8 @@ 159: Done 159: ----------------- Test AND queries 159: Done -215/236 Test #159: moldraw2DTest1 ......................... Passed 11.17 sec -216/236 Test #186: testRGroupDecomp ....................... Passed 9.98 sec -177: VS001: PASSED -177: VS002: PASSED -177: VS003: PASSED -177: VS004: PASSED -177: VS005: PASSED -177: VS006: PASSED -177: VS007: PASSED -177: VS008: PASSED -177: VS009: PASSED -177: VS010: PASSED -177: VS011: PASSED -177: VS012: PASSED -177: VS013: PASSED -177: VS014: PASSED -177: VS015: PASSED -177: VS016: PASSED -177: VS017: PASSED -177: VS018: PASSED -177: VS019: PASSED -177: VS020: PASSED -177: VS021: PASSED -177: VS022: PASSED -177: VS023: PASSED -177: VS024: PASSED -177: VS025: PASSED -177: VS026: PASSED -177: VS027: PASSED -177: VS028: PASSED -177: VS029: PASSED -177: VS030: PASSED -177: VS031: PASSED -177: VS032: PASSED -177: VS033: PASSED -177: VS034: PASSED -177: VS035: PASSED -177: VS036: PASSED -177: VS037: PASSED -177: VS038: PASSED -177: VS039: PASSED -177: VS040: PASSED -177: VS041: PASSED -177: VS042: PASSED -177: VS043: PASSED -177: VS044: PASSED -177: VS045: PASSED -177: VS046: PASSED -177: VS047: PASSED -177: VS048: PASSED -177: VS049: PASSED -177: VS050: PASSED -177: VS051: PASSED -177: VS052: PASSED -177: VS053: PASSED -177: VS054: PASSED -177: VS055: PASSED -177: VS056: PASSED -177: VS057: PASSED -177: VS058: PASSED -177: VS059: PASSED -177: VS060: PASSED -177: VS061: PASSED -177: VS062: PASSED -177: VS063: PASSED -177: VS064: PASSED -177: VS065: PASSED -177: VS066: PASSED -177: VS067: PASSED -177: VS068: PASSED -177: VS069: PASSED -177: VS070: PASSED -177: VS071: PASSED -177: VS072: PASSED -177: VS073: PASSED -177: VS074: PASSED -177: VS075: PASSED -177: VS076: PASSED -177: VS077: PASSED -177: VS078: PASSED -177: VS079: PASSED -177: VS080: PASSED -177: VS081: PASSED -177: VS082: PASSED -177: VS083: PASSED -177: VS084: PASSED -177: VS085: PASSED -177: VS086: PASSED -177: VS087: PASSED -177: VS088: PASSED -177: VS089: PASSED -177: VS090: PASSED -177: VS091: PASSED -177: VS092: PASSED -177: VS093: PASSED -177: VS094: PASSED -177: VS095: PASSED -177: VS096: PASSED -177: VS097: PASSED -177: VS098: PASSED -177: VS099: PASSED -177: VS100: PASSED -177: VS101: PASSED -177: VS102: PASSED -177: VS103: PASSED -177: VS104: PASSED -177: VS105: PASSED -177: VS106: PASSED -177: VS107: PASSED -177: VS108: PASSED -177: VS109: PASSED -177: VS110: PASSED -177: VS111: PASSED -177: VS112: PASSED -177: VS113: PASSED -177: VS114: PASSED -177: VS115: PASSED -177: VS116: PASSED -177: VS117: PASSED -177: VS118: PASSED -177: VS119: PASSED -177: VS120: PASSED -177: VS121: PASSED -177: VS122: PASSED -177: VS123: PASSED -177: VS124: PASSED -177: VS125: PASSED -177: VS126: PASSED -177: VS127: PASSED -177: VS128: PASSED -177: VS129: PASSED -177: VS130: PASSED -177: VS131: PASSED -177: VS132: PASSED -177: VS133: PASSED -177: VS134: PASSED -177: VS135: PASSED -177: VS136: PASSED -177: VS137: PASSED -177: VS138: PASSED -177: VS139: PASSED -177: VS140: PASSED -177: VS141: PASSED -177: VS142: PASSED -177: VS143: PASSED -177: VS144: PASSED -177: VS145: PASSED -177: VS146: PASSED -177: VS147: PASSED -177: VS148: PASSED -177: VS149: PASSED -177: VS150: PASSED -177: VS151: PASSED -177: VS152: PASSED -177: VS153: PASSED -177: VS154: PASSED -177: VS155: PASSED -177: VS156: PASSED -177: VS157: PASSED -177: VS158: PASSED -177: VS159: PASSED -177: VS160: PASSED -177: VS161: PASSED -177: VS162: PASSED -177: VS163: PASSED -177: VS164: PASSED -177: VS165: PASSED -177: VS166: PASSED -177: VS167: PASSED -177: VS168: PASSED -177: VS169: PASSED -177: VS170: PASSED -177: VS171: PASSED -177: VS172: PASSED -177: VS173: PASSED -177: VS174: PASSED -177: VS175: PASSED -177: VS176: PASSED -177: VS177: PASSED -177: VS178: PASSED -177: VS179: PASSED -177: VS180: PASSED -177: VS181: PASSED -177: VS182: PASSED -177: VS183: PASSED -177: VS184: PASSED -177: VS185: PASSED -177: VS186: PASSED -177: VS187: PASSED -177: VS188: PASSED -177: VS189: PASSED -177: VS190: PASSED -177: VS191: PASSED -177: VS192: PASSED -177: VS193: PASSED -177: VS194: PASSED -177: VS195: PASSED -177: VS196: PASSED -177: VS197: PASSED -177: VS198: PASSED -177: VS199: PASSED -177: VS200: PASSED -177: VS201: PASSED -177: VS202: PASSED -177: VS203: PASSED -177: VS204: PASSED -177: VS205: PASSED -177: VS206: PASSED -177: VS207: PASSED -177: VS208: PASSED -177: VS209: PASSED -177: VS210: PASSED -177: VS211: PASSED -177: VS212: PASSED -177: VS213: PASSED -177: VS214: PASSED -177: VS215: PASSED -177: VS216: PASSED -177: VS217: PASSED -177: VS218: PASSED -177: VS219: PASSED -177: VS220: PASSED -177: VS221: PASSED -177: VS222: PASSED -177: VS223: PASSED -177: VS224: PASSED -177: VS225: PASSED -177: VS226: PASSED -177: VS227: PASSED -177: VS228: PASSED -177: VS229: PASSED -177: VS230: PASSED -177: VS231: PASSED -177: VS232: PASSED -177: VS233: PASSED -177: VS234: PASSED -177: VS235: PASSED -177: VS236: PASSED -177: VS237: PASSED -177: VS238: PASSED -177: VS239: PASSED -177: VS240: PASSED -177: VS241: PASSED -177: VS242: PASSED -177: VS243: PASSED -177: VS244: PASSED -177: VS245: PASSED -177: VS246: PASSED -177: VS247: PASSED -177: VS248: PASSED -177: VS249: PASSED -177: VS250: PASSED -177: VS251: PASSED -177: VS252: PASSED -177: VS253: PASSED -177: VS254: PASSED -177: VS255: PASSED -177: VS256: PASSED -177: VS257: PASSED -177: VS258: PASSED -177: VS259: PASSED -177: VS260: PASSED -177: VS261: PASSED -177: VS262: PASSED -177: VS263: PASSED -177: VS264: PASSED -177: VS265: PASSED -177: VS266: PASSED -177: VS267: PASSED -177: VS268: PASSED -177: VS269: PASSED -177: VS270: PASSED -177: VS271: PASSED -177: VS272: PASSED -177: VS273: PASSED -177: VS274: PASSED -177: VS275: PASSED -177: VS276: PASSED -177: VS277: PASSED -177: VS278: PASSED -177: VS279: PASSED -177: VS280: PASSED -177: VS281: PASSED -177: VS282: PASSED -177: VS283: PASSED -177: VS284: PASSED -177: VS285: PASSED -177: VS286: PASSED -177: VS287: PASSED -177: VS288: PASSED -177: VS289: PASSED -177: VS290: PASSED -177: VS291: PASSED -177: VS292: PASSED -177: VS293: PASSED -177: VS294: PASSED -177: VS295: PASSED -177: VS296: PASSED -177: VS297: PASSED -177: VS298: PASSED -177: VS299: PASSED -177: VS300: PASSED -177: Check finished: 0 molecules failed. -177: Failed: -217/236 Test #177: pyCIPLabelsValidation .................. Passed 10.66 sec -170: Randomness seeded to: 1757155195 -170: [17:55:31] Timed out after 11 seconds. -152: .............[17:55:32] Molecule does not have explicit Hs. Consider calling AddHs() -152: [17:55:32] Molecule does not have explicit Hs. Consider calling AddHs() -152: [17:55:32] Molecule does not have explicit Hs. Consider calling AddHs() -152: [17:55:32] Molecule does not have explicit Hs. Consider calling AddHs() -152: [17:55:32] Molecule does not have explicit Hs. Consider calling AddHs() -152: [17:55:32] Molecule does not have explicit Hs. Consider calling AddHs() -152: [17:55:32] Molecule does not have explicit Hs. Consider calling AddHs() -152: [17:55:32] Molecule does not have explicit Hs. Consider calling AddHs() -152: [17:55:32] Molecule does not have explicit Hs. Consider calling AddHs() -152: [17:55:32] Molecule does not have explicit Hs. Consider calling AddHs() -152: [17:55:32] Molecule does not have explicit Hs. Consider calling AddHs() -185: ......[17:55:33] -185: -185: **** -185: Pre-condition Violation -185: RingInfo not initialized -185: Violation occurred on line 52 in file ./Code/GraphMol/RingInfo.cpp -185: Failed Expression: df_init -185: ---------- -185: Stacktrace: -185: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -185: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -185: 2# RDKit::RingInfo::numAtomRings(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -185: 3# RDKit::AtomRingQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 -185: 4# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -185: 5# RDKit::atomCompat(RDKit::Atom const*, RDKit::Atom const*, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -185: 6# boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::IsFeasiblePair(unsigned int, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -185: 7# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -185: 8# bool boost::vf2_all, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor, std::vector, std::allocator > >, std::allocator, std::allocator > > > > >(boost::adjacency_list const&, boost::adjacency_list const&, RDKit::detail::AtomLabelFunctor&, RDKit::detail::BondLabelFunctor&, RDKit::MolMatchFinalCheckFunctor&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -185: 9# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -185: 10# bool RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >&, bool, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -185: 11# bool RDKit::HasSubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, bool, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -185: 12# 0x00007F266445D1D5 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -185: 13# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -185: 14# 0x00007F26668F462C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -185: 15# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -185: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so -185: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so -185: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so -185: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -185: 20# 0x00007F26643B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -185: 21# 0x00007F26643B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -185: 22# 0x00007F26643B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -185: 23# 0x00007F26643B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -185: 24# 0x00007F26643B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -185: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so -185: 26# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so -185: 27# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so -185: 28# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so -185: 29# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -185: 30# 0x00007F26668F13C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -185: 31# _PyObject_MakeTpCall in /usr/bin/python3 -185: 32# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 33# 0x00000000005CD3C9 in /usr/bin/python3 -185: 34# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 35# 0x0000000000690C6F in /usr/bin/python3 -185: 36# 0x000000000062D590 in /usr/bin/python3 -185: 37# _PyObject_MakeTpCall in /usr/bin/python3 -185: 38# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 39# 0x00000000005CD3C9 in /usr/bin/python3 -185: 40# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 41# 0x0000000000690C6F in /usr/bin/python3 -185: 42# 0x000000000062D590 in /usr/bin/python3 -185: 43# _PyObject_MakeTpCall in /usr/bin/python3 -185: 44# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 45# 0x00000000005CD3C9 in /usr/bin/python3 -185: 46# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 47# 0x0000000000690C6F in /usr/bin/python3 -185: 48# 0x000000000062D590 in /usr/bin/python3 -185: 49# _PyObject_MakeTpCall in /usr/bin/python3 -185: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 51# 0x00000000005A090C in /usr/bin/python3 -185: 52# _PyObject_MakeTpCall in /usr/bin/python3 -185: 53# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 54# PyEval_EvalCode in /usr/bin/python3 -185: 55# 0x00000000006AB8D1 in /usr/bin/python3 -185: 56# 0x00000000006A899C in /usr/bin/python3 -185: 57# 0x00000000006B9943 in /usr/bin/python3 -185: 58# 0x00000000006B93E3 in /usr/bin/python3 -185: 59# 0x00000000006B921E in /usr/bin/python3 -185: 60# Py_RunMain in /usr/bin/python3 -185: 61# Py_BytesMain in /usr/bin/python3 -185: 62# 0x00007F2667237CA8 in /lib/x86_64-linux-gnu/libc.so.6 -185: 63# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -185: 64# _start in /usr/bin/python3 -185: ---------- -185: **** -185: -185: [17:55:33] -185: -185: **** -185: Pre-condition Violation -185: RingInfo not initialized -185: Violation occurred on line 129 in file ./Code/GraphMol/RingInfo.cpp -185: Failed Expression: df_init -185: ---------- -185: Stacktrace: -185: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -185: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -185: 2# RDKit::RingInfo::numBondRings(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -185: 3# 0x00007F2663EE6800 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -185: 4# Queries::EqualityQuery::Match(RDKit::Bond const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -185: 5# RDKit::bondCompat(RDKit::Bond const*, RDKit::Bond const*, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -185: 6# boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::IsFeasiblePair(unsigned int, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -185: 7# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -185: 8# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -185: 9# bool boost::vf2_all, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor, std::vector, std::allocator > >, std::allocator, std::allocator > > > > >(boost::adjacency_list const&, boost::adjacency_list const&, RDKit::detail::AtomLabelFunctor&, RDKit::detail::BondLabelFunctor&, RDKit::MolMatchFinalCheckFunctor&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -185: 10# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -185: 11# bool RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >&, bool, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -185: 12# bool RDKit::HasSubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, bool, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -185: 13# 0x00007F266445D1D5 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -185: 14# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -185: 15# 0x00007F26668F462C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -185: 16# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -185: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so -185: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so -185: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so -185: 20# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -185: 21# 0x00007F26643B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -185: 22# 0x00007F26643B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -185: 23# 0x00007F26643B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -185: 24# 0x00007F26643B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -185: 25# 0x00007F26643B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -185: 26# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so -185: 27# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so -185: 28# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so -185: 29# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so -185: 30# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -185: 31# 0x00007F26668F13C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -185: 32# _PyObject_MakeTpCall in /usr/bin/python3 -185: 33# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 34# 0x00000000005CD3C9 in /usr/bin/python3 -185: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 36# 0x0000000000690C6F in /usr/bin/python3 -185: 37# 0x000000000062D590 in /usr/bin/python3 -185: 38# _PyObject_MakeTpCall in /usr/bin/python3 -185: 39# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 40# 0x00000000005CD3C9 in /usr/bin/python3 -185: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 42# 0x0000000000690C6F in /usr/bin/python3 -185: 43# 0x000000000062D590 in /usr/bin/python3 -185: 44# _PyObject_MakeTpCall in /usr/bin/python3 -185: 45# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 46# 0x00000000005CD3C9 in /usr/bin/python3 -185: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 48# 0x0000000000690C6F in /usr/bin/python3 -185: 49# 0x000000000062D590 in /usr/bin/python3 -185: 50# _PyObject_MakeTpCall in /usr/bin/python3 -185: 51# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 52# 0x00000000005A090C in /usr/bin/python3 -185: 53# _PyObject_MakeTpCall in /usr/bin/python3 -185: 54# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 55# PyEval_EvalCode in /usr/bin/python3 -185: 56# 0x00000000006AB8D1 in /usr/bin/python3 -185: 57# 0x00000000006A899C in /usr/bin/python3 -185: 58# 0x00000000006B9943 in /usr/bin/python3 -185: 59# 0x00000000006B93E3 in /usr/bin/python3 -185: 60# 0x00000000006B921E in /usr/bin/python3 -185: 61# Py_RunMain in /usr/bin/python3 -185: 62# Py_BytesMain in /usr/bin/python3 -185: 63# 0x00007F2667237CA8 in /lib/x86_64-linux-gnu/libc.so.6 -185: 64# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -185: 65# _start in /usr/bin/python3 -185: ---------- -185: **** -185: -183: [17:55:33] ------------------------------------- -183: [17:55:33] Results do not depend on numThreads (all same) -183: [17:55:33] ------------------------------------- -183: [17:55:33] testTautomerQueries -183: [17:55:33] Pattern fingerprints for tautomersearch aren't tautomer fingerprints, ignoring... -183: [17:55:33] ------------------------------------- -183: [17:55:33] github3881 recursive smarts with rings -218/236 Test #183: substructLibraryTest ................... Passed 11.96 sec -95: 0,0 0 -95: 0,1 0 -95: 1,0 0 -95: 1,1 0 -95: 2,0 0 -95: 2,1 0 -219/236 Test #95: testEnumeration ........................ Passed 14.15 sec -195: ..[17:55:34] +216/236 Test #159: moldraw2DTest1 ......................... Passed 25.59 sec +195: ..[14:18:07] 195: 195: **** 195: Pre-condition Violation @@ -34099,7 +33654,7 @@ 195: 2# RDKit::Atom::getOwningMol() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 3# boost::python::objects::caller_py_function_impl, boost::mpl::vector2 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -195: 5# 0x00007F81AA8A162C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 5# 0x00007FE6AF4E762C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 195: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34110,17 +33665,17 @@ 195: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 195: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 195: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 16# 0x00007F81A7FB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 17# 0x00007F81A7FB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 18# 0x00007F81A7FB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 19# 0x00007F81A7FB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 20# 0x00007F81A7FB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 16# 0x00007FE6ACBB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 17# 0x00007FE6ACBB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 18# 0x00007FE6ACBB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 19# 0x00007FE6ACBB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 20# 0x00007FE6ACBB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 25# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -195: 26# 0x00007F81AA89E3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 26# 0x00007FE6AF4E43C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 27# _PyObject_MakeTpCall in /usr/bin/python3 195: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 29# 0x00000000005CD3C9 in /usr/bin/python3 @@ -34152,13 +33707,13 @@ 195: 55# 0x00000000006B921E in /usr/bin/python3 195: 56# Py_RunMain in /usr/bin/python3 195: 57# Py_BytesMain in /usr/bin/python3 -195: 58# 0x00007F81AB07BCA8 in /lib/x86_64-linux-gnu/libc.so.6 +195: 58# 0x00007FE6AFCC1CA8 in /lib/x86_64-linux-gnu/libc.so.6 195: 59# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 195: 60# _start in /usr/bin/python3 195: ---------- 195: **** 195: -195: [17:55:34] +195: [14:18:07] 195: 195: **** 195: Pre-condition Violation @@ -34172,7 +33727,7 @@ 195: 2# RDKit::AtomGetNeighbors(RDKit::Atom*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -195: 5# 0x00007F81AA8A162C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 5# 0x00007FE6AF4E762C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 195: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34183,17 +33738,17 @@ 195: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 195: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 195: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 16# 0x00007F81A7FB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 17# 0x00007F81A7FB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 18# 0x00007F81A7FB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 19# 0x00007F81A7FB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 20# 0x00007F81A7FB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 16# 0x00007FE6ACBB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 17# 0x00007FE6ACBB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 18# 0x00007FE6ACBB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 19# 0x00007FE6ACBB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 20# 0x00007FE6ACBB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 25# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -195: 26# 0x00007F81AA89E3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 26# 0x00007FE6AF4E43C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 27# _PyObject_MakeTpCall in /usr/bin/python3 195: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 29# 0x00000000005CD3C9 in /usr/bin/python3 @@ -34225,13 +33780,13 @@ 195: 55# 0x00000000006B921E in /usr/bin/python3 195: 56# Py_RunMain in /usr/bin/python3 195: 57# Py_BytesMain in /usr/bin/python3 -195: 58# 0x00007F81AB07BCA8 in /lib/x86_64-linux-gnu/libc.so.6 +195: 58# 0x00007FE6AFCC1CA8 in /lib/x86_64-linux-gnu/libc.so.6 195: 59# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 195: 60# _start in /usr/bin/python3 195: ---------- 195: **** 195: -195: [17:55:34] +195: [14:18:07] 195: 195: **** 195: Pre-condition Violation @@ -34245,7 +33800,7 @@ 195: 2# RDKit::AtomGetBonds(RDKit::Atom*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -195: 5# 0x00007F81AA8A162C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 5# 0x00007FE6AF4E762C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 195: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34256,17 +33811,17 @@ 195: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 195: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 195: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 16# 0x00007F81A7FB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 17# 0x00007F81A7FB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 18# 0x00007F81A7FB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 19# 0x00007F81A7FB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 20# 0x00007F81A7FB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 16# 0x00007FE6ACBB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 17# 0x00007FE6ACBB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 18# 0x00007FE6ACBB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 19# 0x00007FE6ACBB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 20# 0x00007FE6ACBB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 25# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -195: 26# 0x00007F81AA89E3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 26# 0x00007FE6AF4E43C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 27# _PyObject_MakeTpCall in /usr/bin/python3 195: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 29# 0x00000000005CD3C9 in /usr/bin/python3 @@ -34298,13 +33853,13 @@ 195: 55# 0x00000000006B921E in /usr/bin/python3 195: 56# Py_RunMain in /usr/bin/python3 195: 57# Py_BytesMain in /usr/bin/python3 -195: 58# 0x00007F81AB07BCA8 in /lib/x86_64-linux-gnu/libc.so.6 +195: 58# 0x00007FE6AFCC1CA8 in /lib/x86_64-linux-gnu/libc.so.6 195: 59# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 195: 60# _start in /usr/bin/python3 195: ---------- 195: **** 195: -195: [17:55:34] +195: [14:18:07] 195: 195: **** 195: Pre-condition Violation @@ -34318,7 +33873,7 @@ 195: 2# RDKit::AtomIsInRing(RDKit::Atom const*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -195: 5# 0x00007F81AA8A162C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 5# 0x00007FE6AF4E762C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 195: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34329,17 +33884,17 @@ 195: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 195: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 195: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 16# 0x00007F81A7FB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 17# 0x00007F81A7FB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 18# 0x00007F81A7FB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 19# 0x00007F81A7FB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 20# 0x00007F81A7FB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 16# 0x00007FE6ACBB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 17# 0x00007FE6ACBB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 18# 0x00007FE6ACBB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 19# 0x00007FE6ACBB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 20# 0x00007FE6ACBB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 25# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -195: 26# 0x00007F81AA89E3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 26# 0x00007FE6AF4E43C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 27# _PyObject_MakeTpCall in /usr/bin/python3 195: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 29# 0x00000000005CD3C9 in /usr/bin/python3 @@ -34371,13 +33926,13 @@ 195: 55# 0x00000000006B921E in /usr/bin/python3 195: 56# Py_RunMain in /usr/bin/python3 195: 57# Py_BytesMain in /usr/bin/python3 -195: 58# 0x00007F81AB07BCA8 in /lib/x86_64-linux-gnu/libc.so.6 +195: 58# 0x00007FE6AFCC1CA8 in /lib/x86_64-linux-gnu/libc.so.6 195: 59# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 195: 60# _start in /usr/bin/python3 195: ---------- 195: **** 195: -195: [17:55:34] +195: [14:18:07] 195: 195: **** 195: Pre-condition Violation @@ -34391,7 +33946,7 @@ 195: 2# RDKit::AtomIsInRingSize(RDKit::Atom const*, int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -195: 5# 0x00007F81AA8A162C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 5# 0x00007FE6AF4E762C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 195: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34402,17 +33957,17 @@ 195: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 195: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 195: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 16# 0x00007F81A7FB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 17# 0x00007F81A7FB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 18# 0x00007F81A7FB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 19# 0x00007F81A7FB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 20# 0x00007F81A7FB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 16# 0x00007FE6ACBB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 17# 0x00007FE6ACBB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 18# 0x00007FE6ACBB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 19# 0x00007FE6ACBB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 20# 0x00007FE6ACBB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 25# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -195: 26# 0x00007F81AA89E3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 26# 0x00007FE6AF4E43C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 27# _PyObject_MakeTpCall in /usr/bin/python3 195: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 29# 0x00000000005CD3C9 in /usr/bin/python3 @@ -34444,13 +33999,13 @@ 195: 55# 0x00000000006B921E in /usr/bin/python3 195: 56# Py_RunMain in /usr/bin/python3 195: 57# Py_BytesMain in /usr/bin/python3 -195: 58# 0x00007F81AB07BCA8 in /lib/x86_64-linux-gnu/libc.so.6 +195: 58# 0x00007FE6AFCC1CA8 in /lib/x86_64-linux-gnu/libc.so.6 195: 59# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 195: 60# _start in /usr/bin/python3 195: ---------- 195: **** 195: -195: .....[17:55:34] +195: .....[14:18:07] 195: 195: **** 195: Range Error @@ -34464,7 +34019,7 @@ 195: 2# RDKit::RWMol::addBond(unsigned int, unsigned int, RDKit::Bond::BondType) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 195: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -195: 5# 0x00007F81AA8A162C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 5# 0x00007FE6AF4E762C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 195: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34475,17 +34030,17 @@ 195: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 195: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 195: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 16# 0x00007F81A7FB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 17# 0x00007F81A7FB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 18# 0x00007F81A7FB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 19# 0x00007F81A7FB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 20# 0x00007F81A7FB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 16# 0x00007FE6ACBB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 17# 0x00007FE6ACBB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 18# 0x00007FE6ACBB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 19# 0x00007FE6ACBB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 20# 0x00007FE6ACBB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 25# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -195: 26# 0x00007F81AA89E3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 26# 0x00007FE6AF4E43C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 27# _PyObject_MakeTpCall in /usr/bin/python3 195: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 29# 0x00000000005CD3C9 in /usr/bin/python3 @@ -34517,49 +34072,49 @@ 195: 55# 0x00000000006B921E in /usr/bin/python3 195: 56# Py_RunMain in /usr/bin/python3 195: 57# Py_BytesMain in /usr/bin/python3 -195: 58# 0x00007F81AB07BCA8 in /lib/x86_64-linux-gnu/libc.so.6 +195: 58# 0x00007FE6AFCC1CA8 in /lib/x86_64-linux-gnu/libc.so.6 195: 59# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 195: 60# _start in /usr/bin/python3 195: ---------- 195: **** 195: -195: ......[17:55:34] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -195: [17:55:34] ERROR: Smiles parse error on line 0 -195: [17:55:34] ERROR: Cannot create molecule from : 'c1ccccc' -195: [17:55:34] SMILES Parse Error: extra open parentheses while parsing: C(C -195: [17:55:34] SMILES Parse Error: check for mistakes around position 2: -195: [17:55:34] C(C -195: [17:55:34] ~^ -195: [17:55:34] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' -195: [17:55:34] ERROR: Smiles parse error on line 3 -195: [17:55:34] ERROR: Cannot create molecule from : 'C(C' -195: [17:55:34] Explicit valence for atom # 1 C, 5, is greater than permitted -195: [17:55:34] ERROR: Could not sanitize molecule on line 6 -195: [17:55:34] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted -195: [17:55:34] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -195: [17:55:34] ERROR: Smiles parse error on line 0 -195: [17:55:34] ERROR: Cannot create molecule from : 'c1ccccc' -195: [17:55:34] SMILES Parse Error: extra open parentheses while parsing: C(C -195: [17:55:34] SMILES Parse Error: check for mistakes around position 2: -195: [17:55:34] C(C -195: [17:55:34] ~^ -195: [17:55:34] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' -195: [17:55:34] ERROR: Smiles parse error on line 3 -195: [17:55:34] ERROR: Cannot create molecule from : 'C(C' -195: [17:55:34] SMILES Parse Error: unclosed ring for input: 'C1C(Cl)CCCC' -195: [17:55:34] ERROR: Smiles parse error on line 6 -195: [17:55:34] ERROR: Cannot create molecule from : 'C1C(Cl)CCCC' -195: [17:55:34] Explicit valence for atom # 1 F, 2, is greater than permitted -195: [17:55:34] ERROR: Could not sanitize molecule ending on line 21 -195: [17:55:34] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -195: [17:55:34] ERROR: EOF hit while reading atoms -195: [17:55:34] ERROR: moving to the beginning of the next molecule -195: [17:55:34] Explicit valence for atom # 1 F, 2, is greater than permitted -195: [17:55:34] ERROR: Could not sanitize molecule ending on line 21 -195: [17:55:34] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -195: [17:55:34] ERROR: EOF hit while reading atoms -195: [17:55:34] ERROR: moving to the beginning of the next molecule -195: ....[17:55:34] +195: ......[14:18:07] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +195: [14:18:07] ERROR: Smiles parse error on line 0 +195: [14:18:07] ERROR: Cannot create molecule from : 'c1ccccc' +195: [14:18:07] SMILES Parse Error: extra open parentheses while parsing: C(C +195: [14:18:07] SMILES Parse Error: check for mistakes around position 2: +195: [14:18:07] C(C +195: [14:18:07] ~^ +195: [14:18:07] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' +195: [14:18:07] ERROR: Smiles parse error on line 3 +195: [14:18:07] ERROR: Cannot create molecule from : 'C(C' +195: [14:18:07] Explicit valence for atom # 1 C, 5, is greater than permitted +195: [14:18:07] ERROR: Could not sanitize molecule on line 6 +195: [14:18:07] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted +195: [14:18:07] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +195: [14:18:07] ERROR: Smiles parse error on line 0 +195: [14:18:07] ERROR: Cannot create molecule from : 'c1ccccc' +195: [14:18:07] SMILES Parse Error: extra open parentheses while parsing: C(C +195: [14:18:07] SMILES Parse Error: check for mistakes around position 2: +195: [14:18:07] C(C +195: [14:18:07] ~^ +195: [14:18:07] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' +195: [14:18:07] ERROR: Smiles parse error on line 3 +195: [14:18:07] ERROR: Cannot create molecule from : 'C(C' +195: [14:18:07] SMILES Parse Error: unclosed ring for input: 'C1C(Cl)CCCC' +195: [14:18:07] ERROR: Smiles parse error on line 6 +195: [14:18:07] ERROR: Cannot create molecule from : 'C1C(Cl)CCCC' +195: [14:18:07] Explicit valence for atom # 1 F, 2, is greater than permitted +195: [14:18:07] ERROR: Could not sanitize molecule ending on line 21 +195: [14:18:07] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +195: [14:18:07] ERROR: EOF hit while reading atoms +195: [14:18:07] ERROR: moving to the beginning of the next molecule +195: [14:18:07] Explicit valence for atom # 1 F, 2, is greater than permitted +195: [14:18:07] ERROR: Could not sanitize molecule ending on line 21 +195: [14:18:07] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +195: [14:18:07] ERROR: EOF hit while reading atoms +195: [14:18:07] ERROR: moving to the beginning of the next molecule +195: ....[14:18:07] 195: 195: **** 195: Pre-condition Violation @@ -34573,7 +34128,7 @@ 195: 2# RDKit::RingInfo::numRings() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 195: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -195: 5# 0x00007F81AA8A162C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 5# 0x00007FE6AF4E762C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 195: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34584,17 +34139,17 @@ 195: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 195: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 195: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 16# 0x00007F81A7FB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 17# 0x00007F81A7FB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 18# 0x00007F81A7FB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 19# 0x00007F81A7FB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 20# 0x00007F81A7FB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 16# 0x00007FE6ACBB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 17# 0x00007FE6ACBB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 18# 0x00007FE6ACBB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 19# 0x00007FE6ACBB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 20# 0x00007FE6ACBB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 25# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -195: 26# 0x00007F81AA89E3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 26# 0x00007FE6AF4E43C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 27# _PyObject_MakeTpCall in /usr/bin/python3 195: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 29# 0x00000000005CD3C9 in /usr/bin/python3 @@ -34626,13 +34181,13 @@ 195: 55# 0x00000000006B921E in /usr/bin/python3 195: 56# Py_RunMain in /usr/bin/python3 195: 57# Py_BytesMain in /usr/bin/python3 -195: 58# 0x00007F81AB07BCA8 in /lib/x86_64-linux-gnu/libc.so.6 +195: 58# 0x00007FE6AFCC1CA8 in /lib/x86_64-linux-gnu/libc.so.6 195: 59# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 195: 60# _start in /usr/bin/python3 195: ---------- 195: **** 195: -195: .............[17:55:34] +195: .............[14:18:07] 195: 195: **** 195: Range Error @@ -34646,7 +34201,7 @@ 195: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 195: 3# boost::python::objects::caller_py_function_impl >, boost::mpl::vector3 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -195: 5# 0x00007F81AA8A162C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 5# 0x00007FE6AF4E762C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 195: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34657,17 +34212,17 @@ 195: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 195: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 195: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 16# 0x00007F81A7FB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 17# 0x00007F81A7FB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 18# 0x00007F81A7FB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 19# 0x00007F81A7FB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 20# 0x00007F81A7FB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 16# 0x00007FE6ACBB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 17# 0x00007FE6ACBB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 18# 0x00007FE6ACBB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 19# 0x00007FE6ACBB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 20# 0x00007FE6ACBB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 25# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -195: 26# 0x00007F81AA89E3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 26# 0x00007FE6AF4E43C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 27# _PyObject_MakeTpCall in /usr/bin/python3 195: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 29# 0x00000000005CD3C9 in /usr/bin/python3 @@ -34699,139 +34254,602 @@ 195: 55# 0x00000000006B921E in /usr/bin/python3 195: 56# Py_RunMain in /usr/bin/python3 195: 57# Py_BytesMain in /usr/bin/python3 -195: 58# 0x00007F81AB07BCA8 in /lib/x86_64-linux-gnu/libc.so.6 +195: 58# 0x00007FE6AFCC1CA8 in /lib/x86_64-linux-gnu/libc.so.6 195: 59# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 195: 60# _start in /usr/bin/python3 195: ---------- 195: **** 195: -195: ...[17:55:34] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -195: ............................[17:55:34] SMILES Parse Error: unclosed ring for input: 'C1CC' +195: ...[14:18:07] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +195: ............................[14:18:07] SMILES Parse Error: unclosed ring for input: 'C1CC' 195: ......smi: CC1=C(n2cccc2[C@H](C)Cl)C(C)CCC1 |(2.679,0.4142,;1.3509,1.181,;0.0229,0.4141,;0.0229,-1.1195,;1.2645,-2.0302,;0.7901,-3.4813,;-0.7446,-3.4813,;-1.219,-2.0302,;-2.679,-1.5609,;-3.0039,-0.0556,;-3.8202,-2.595,;-1.3054,1.1809,;-2.6335,0.4141,;-1.3054,2.7145,;0.0229,3.4813,;1.3509,2.7146,),wD:8.9,2.11,a:2,&1:8| -195: 863 -195: ..[17:55:34] WARNING: not removing hydrogen atom without neighbors -195: [17:55:34] WARNING: not removing hydrogen atom with dummy atom neighbors -195: [17:55:34] WARNING: not removing hydrogen atom with wedged bond -195: [17:55:34] WARNING: not removing hydrogen atom without neighbors -195: [17:55:34] WARNING: not removing hydrogen atom with dummy atom neighbors -29: Checking against /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -29: All 191 tests passed -29: done -29: ------------------------------------- -29: Unit tests for all MMFF constraint terms. -195: ......[17:55:38] Explicit valence for atom # 1 F, 2, is greater than permitted -195: [17:55:38] Can't kekulize mol. Unkekulized atoms: 0 1 2 -195: .[17:55:38] Explicit valence for atom # 1 F, 2, is greater than permitted -195: [17:55:38] Explicit valence for atom # 1 F, 2, is greater than permitted -195: [17:55:38] Explicit valence for atom # 1 F, 2, is greater than permitted -195: [17:55:38] Explicit valence for atom # 1 F, 2, is greater than permitted -195: [17:55:38] Can't kekulize mol. Unkekulized atoms: 0 1 2 -195: [17:55:38] Can't kekulize mol. Unkekulized atoms: 0 1 2 -195: [17:55:38] Can't kekulize mol. Unkekulized atoms: 0 1 2 -29: 10.0003 -195: ..........[17:55:38] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname -195: [17:55:38] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' -195: .[17:55:38] SMILES Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname -195: [17:55:38] SMILES Parse Error: check for mistakes around position 4: -195: [17:55:38] CCC |$foo;;bar$| ourname -195: [17:55:38] ~~~^ -195: [17:55:38] SMILES Parse Error: Failed parsing SMILES 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' -195: ..[17:55:38] SMILES Parse Error: syntax error while parsing: error -195: [17:55:38] SMILES Parse Error: check for mistakes around position 1: -195: [17:55:38] error -195: [17:55:38] ^ -195: [17:55:38] SMILES Parse Error: Failed parsing SMILES 'error' for input: 'error' -195: [17:55:38] SMILES Parse Error: Failed parsing SMILES 'd' for input: 'd' -195: [17:55:38] SMARTS Parse Error: Failed parsing SMARTS 'error' for input: 'error' -195: [17:55:38] SMARTS Parse Error: Failed parsing SMARTS 'd' for input: 'd' -29: done -29: ------------------------------------- -29: Unit test for MMFF TorsionConstraint close to 0 degrees. -29: done -29: ------------------------------------- -29: Unit tests for copying MMFF ForceFields. -29: done -29: ------------------------------------- -29: Unit test for MMFF butane scan. -152: ...[17:55:38] Molecule does not have explicit Hs. Consider calling AddHs() -152: [17:55:38] Molecule does not have explicit Hs. Consider calling AddHs() -152: [17:55:38] Molecule does not have explicit Hs. Consider calling AddHs() -152: [17:55:38] Molecule does not have explicit Hs. Consider calling AddHs() -152: [17:55:38] Molecule does not have explicit Hs. Consider calling AddHs() -152: ... -152: ---------------------------------------------------------------------- -152: Ran 19 tests in 17.580s -152: -152: OK -152: Testing MolAlign Wrappers -195: .........................[17:55:38] SMILES Parse Error: syntax error while parsing: garbage_0 -195: [17:55:38] SMILES Parse Error: check for mistakes around position 1: -195: [17:55:38] garbage_0 -195: [17:55:38] ^ -195: [17:55:38] SMILES Parse Error: Failed parsing SMILES 'garbage_0' for input: 'garbage_0' -195: [17:55:38] SMILES Parse Error: syntax error while parsing: garbage_2 -195: [17:55:38] SMILES Parse Error: check for mistakes around position 1: -195: [17:55:38] garbage_2 -195: [17:55:38] ^ -195: [17:55:38] SMILES Parse Error: Failed parsing SMILES 'garbage_2' for input: 'garbage_2' -195: [17:55:38] SMILES Parse Error: syntax error while parsing: garbage_4 -195: [17:55:38] SMILES Parse Error: check for mistakes around position 1: -195: [17:55:38] garbage_4 -195: [17:55:38] ^ -195: [17:55:38] SMILES Parse Error: Failed parsing SMILES 'garbage_4' for input: 'garbage_4' +195: 1 +195: ..[14:18:07] WARNING: not removing hydrogen atom without neighbors +195: [14:18:07] WARNING: not removing hydrogen atom with dummy atom neighbors +195: [14:18:07] WARNING: not removing hydrogen atom with wedged bond +195: [14:18:07] WARNING: not removing hydrogen atom without neighbors +195: [14:18:07] WARNING: not removing hydrogen atom with dummy atom neighbors +195: ......[14:18:08] Explicit valence for atom # 1 F, 2, is greater than permitted +195: [14:18:08] Can't kekulize mol. Unkekulized atoms: 0 1 2 +195: .[14:18:08] Explicit valence for atom # 1 F, 2, is greater than permitted +195: [14:18:08] Explicit valence for atom # 1 F, 2, is greater than permitted +195: [14:18:08] Explicit valence for atom # 1 F, 2, is greater than permitted +195: [14:18:08] Explicit valence for atom # 1 F, 2, is greater than permitted +195: [14:18:08] Can't kekulize mol. Unkekulized atoms: 0 1 2 +195: [14:18:08] Can't kekulize mol. Unkekulized atoms: 0 1 2 +195: [14:18:08] Can't kekulize mol. Unkekulized atoms: 0 1 2 +195: ..........[14:18:08] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname +195: [14:18:08] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' +195: .[14:18:08] SMILES Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname +195: [14:18:08] SMILES Parse Error: check for mistakes around position 4: +195: [14:18:08] CCC |$foo;;bar$| ourname +195: [14:18:08] ~~~^ +195: [14:18:08] SMILES Parse Error: Failed parsing SMILES 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' +195: ..[14:18:08] SMILES Parse Error: syntax error while parsing: error +195: [14:18:08] SMILES Parse Error: check for mistakes around position 1: +195: [14:18:08] error +195: [14:18:08] ^ +195: [14:18:08] SMILES Parse Error: Failed parsing SMILES 'error' for input: 'error' +195: [14:18:08] SMILES Parse Error: Failed parsing SMILES 'd' for input: 'd' +195: [14:18:08] SMARTS Parse Error: Failed parsing SMARTS 'error' for input: 'error' +195: [14:18:08] SMARTS Parse Error: Failed parsing SMARTS 'd' for input: 'd' +195: .........................[14:18:09] SMILES Parse Error: syntax error while parsing: garbage_0 +195: [14:18:09] SMILES Parse Error: check for mistakes around position 1: +195: [14:18:09] garbage_0 +195: [14:18:09] ^ +195: [14:18:09] SMILES Parse Error: Failed parsing SMILES 'garbage_0' for input: 'garbage_0' +195: [14:18:09] SMILES Parse Error: syntax error while parsing: garbage_2 +195: [14:18:09] SMILES Parse Error: check for mistakes around position 1: +195: [14:18:09] garbage_2 +195: [14:18:09] ^ +195: [14:18:09] SMILES Parse Error: Failed parsing SMILES 'garbage_2' for input: 'garbage_2' +195: [14:18:09] SMILES Parse Error: syntax error while parsing: garbage_4 +195: [14:18:09] SMILES Parse Error: check for mistakes around position 1: +195: [14:18:09] garbage_4 +195: [14:18:09] ^ +195: [14:18:09] SMILES Parse Error: Failed parsing SMILES 'garbage_4' for input: 'garbage_4' 195: ............ 195: ---------------------------------------------------------------------- -195: Ran 279 tests in 14.702s +195: Ran 279 tests in 20.829s 195: 195: OK 195: supplier: 195: supplier: 195: supplier: -220/236 Test #152: pyMolAlign ............................. Passed 17.92 sec -221/236 Test #195: pyGraphMolWrap ......................... Passed 15.87 sec -29: done -222/236 Test #29: testMMFFForceField ..................... Passed 21.49 sec -185: ............. -185: ---------------------------------------------------------------------- -185: Ran 19 tests in 17.088s -185: -185: OK -185: Testing atom rings -185: testing bond rings -185: searching atom rings -185: searching bond rings -185: done -223/236 Test #185: pySubstructLibrary ..................... Passed 17.41 sec -173: [17:55:40] Complex queries can be slow. -173: [17:55:40] Complex queries can be slow. -173: [17:55:40] Complex queries can be slow. -51: Randomness seeded to: 452291072 +217/236 Test #195: pyGraphMolWrap ......................... Passed 22.96 sec +95: 0,0 0 +95: 0,1 0 +95: 1,0 0 +95: 1,1 0 +95: 2,0 0 +95: 2,1 0 +218/236 Test #95: testEnumeration ........................ Passed 32.11 sec +51: Randomness seeded to: 1537814717 51: =============================================================================== 51: All tests passed (14835 assertions in 14 test cases) 51: -224/236 Test #51: canonTestsCatch ........................ Passed 20.91 sec -173: [17:55:40] Complex queries can be slow. -173: [17:55:40] Complex queries can be slow. -173: [17:55:40] Complex queries can be slow. -173: [17:55:40] Complex queries can be slow. -173: [17:55:40] Complex queries can be slow. -173: [17:55:40] Complex queries can be slow. +219/236 Test #51: canonTestsCatch ........................ Passed 34.10 sec +177: VS001: PASSED +177: VS002: PASSED +177: VS003: PASSED +177: VS004: PASSED +177: VS005: PASSED +177: VS006: PASSED +177: VS007: PASSED +177: VS008: PASSED +177: VS009: PASSED +177: VS010: PASSED +177: VS011: PASSED +177: VS012: PASSED +177: VS013: PASSED +177: VS014: PASSED +177: VS015: PASSED +177: VS016: PASSED +177: VS017: PASSED +177: VS018: PASSED +177: VS019: PASSED +177: VS020: PASSED +177: VS021: PASSED +177: VS022: PASSED +177: VS023: PASSED +177: VS024: PASSED +177: VS025: PASSED +177: VS026: PASSED +177: VS027: PASSED +177: VS028: PASSED +177: VS029: PASSED +177: VS030: PASSED +177: VS031: PASSED +177: VS032: PASSED +177: VS033: PASSED +177: VS034: PASSED +177: VS035: PASSED +177: VS036: PASSED +177: VS037: PASSED +177: VS038: PASSED +177: VS039: PASSED +177: VS040: PASSED +177: VS041: PASSED +177: VS042: PASSED +177: VS043: PASSED +177: VS044: PASSED +177: VS045: PASSED +177: VS046: PASSED +177: VS047: PASSED +177: VS048: PASSED +177: VS049: PASSED +177: VS050: PASSED +177: VS051: PASSED +177: VS052: PASSED +177: VS053: PASSED +177: VS054: PASSED +177: VS055: PASSED +177: VS056: PASSED +177: VS057: PASSED +177: VS058: PASSED +177: VS059: PASSED +177: VS060: PASSED +177: VS061: PASSED +177: VS062: PASSED +177: VS063: PASSED +177: VS064: PASSED +177: VS065: PASSED +177: VS066: PASSED +177: VS067: PASSED +177: VS068: PASSED +177: VS069: PASSED +177: VS070: PASSED +177: VS071: PASSED +177: VS072: PASSED +177: VS073: PASSED +177: VS074: PASSED +177: VS075: PASSED +177: VS076: PASSED +177: VS077: PASSED +177: VS078: PASSED +177: VS079: PASSED +177: VS080: PASSED +177: VS081: PASSED +177: VS082: PASSED +177: VS083: PASSED +177: VS084: PASSED +177: VS085: PASSED +177: VS086: PASSED +177: VS087: PASSED +177: VS088: PASSED +177: VS089: PASSED +177: VS090: PASSED +177: VS091: PASSED +177: VS092: PASSED +177: VS093: PASSED +177: VS094: PASSED +177: VS095: PASSED +177: VS096: PASSED +177: VS097: PASSED +177: VS098: PASSED +177: VS099: PASSED +177: VS100: PASSED +177: VS101: PASSED +177: VS102: PASSED +177: VS103: PASSED +177: VS104: PASSED +177: VS105: PASSED +177: VS106: PASSED +177: VS107: PASSED +177: VS108: PASSED +177: VS109: PASSED +177: VS110: PASSED +177: VS111: PASSED +177: VS112: PASSED +177: VS113: PASSED +177: VS114: PASSED +177: VS115: PASSED +177: VS116: PASSED +177: VS117: PASSED +177: VS118: PASSED +177: VS119: PASSED +177: VS120: PASSED +177: VS121: PASSED +177: VS122: PASSED +177: VS123: PASSED +177: VS124: PASSED +177: VS125: PASSED +177: VS126: PASSED +177: VS127: PASSED +177: VS128: PASSED +177: VS129: PASSED +177: VS130: PASSED +177: VS131: PASSED +177: VS132: PASSED +177: VS133: PASSED +177: VS134: PASSED +177: VS135: PASSED +177: VS136: PASSED +177: VS137: PASSED +177: VS138: PASSED +177: VS139: PASSED +177: VS140: PASSED +177: VS141: PASSED +177: VS142: PASSED +177: VS143: PASSED +177: VS144: PASSED +177: VS145: PASSED +177: VS146: PASSED +177: VS147: PASSED +177: VS148: PASSED +177: VS149: PASSED +177: VS150: PASSED +177: VS151: PASSED +177: VS152: PASSED +177: VS153: PASSED +177: VS154: PASSED +177: VS155: PASSED +177: VS156: PASSED +177: VS157: PASSED +177: VS158: PASSED +177: VS159: PASSED +177: VS160: PASSED +177: VS161: PASSED +177: VS162: PASSED +177: VS163: PASSED +177: VS164: PASSED +177: VS165: PASSED +177: VS166: PASSED +177: VS167: PASSED +177: VS168: PASSED +177: VS169: PASSED +177: VS170: PASSED +177: VS171: PASSED +177: VS172: PASSED +177: VS173: PASSED +177: VS174: PASSED +177: VS175: PASSED +177: VS176: PASSED +177: VS177: PASSED +177: VS178: PASSED +177: VS179: PASSED +177: VS180: PASSED +177: VS181: PASSED +177: VS182: PASSED +177: VS183: PASSED +177: VS184: PASSED +177: VS185: PASSED +177: VS186: PASSED +177: VS187: PASSED +177: VS188: PASSED +177: VS189: PASSED +177: VS190: PASSED +177: VS191: PASSED +177: VS192: PASSED +177: VS193: PASSED +177: VS194: PASSED +177: VS195: PASSED +177: VS196: PASSED +177: VS197: PASSED +177: VS198: PASSED +177: VS199: PASSED +177: VS200: PASSED +177: VS201: PASSED +177: VS202: PASSED +177: VS203: PASSED +177: VS204: PASSED +177: VS205: PASSED +177: VS206: PASSED +177: VS207: PASSED +177: VS208: PASSED +177: VS209: PASSED +177: VS210: PASSED +177: VS211: PASSED +177: VS212: PASSED +177: VS213: PASSED +177: VS214: PASSED +177: VS215: PASSED +177: VS216: PASSED +177: VS217: PASSED +177: VS218: PASSED +177: VS219: PASSED +177: VS220: PASSED +177: VS221: PASSED +177: VS222: PASSED +177: VS223: PASSED +177: VS224: PASSED +177: VS225: PASSED +177: VS226: PASSED +177: VS227: PASSED +177: VS228: PASSED +177: VS229: PASSED +177: VS230: PASSED +177: VS231: PASSED +177: VS232: PASSED +177: VS233: PASSED +177: VS234: PASSED +177: VS235: PASSED +177: VS236: PASSED +177: VS237: PASSED +177: VS238: PASSED +177: VS239: PASSED +177: VS240: PASSED +177: VS241: PASSED +177: VS242: PASSED +177: VS243: PASSED +177: VS244: PASSED +177: VS245: PASSED +177: VS246: PASSED +177: VS247: PASSED +177: VS248: PASSED +177: VS249: PASSED +177: VS250: PASSED +177: VS251: PASSED +177: VS252: PASSED +177: VS253: PASSED +177: VS254: PASSED +177: VS255: PASSED +177: VS256: PASSED +177: VS257: PASSED +177: VS258: PASSED +177: VS259: PASSED +177: VS260: PASSED +177: VS261: PASSED +177: VS262: PASSED +177: VS263: PASSED +177: VS264: PASSED +177: VS265: PASSED +177: VS266: PASSED +177: VS267: PASSED +177: VS268: PASSED +177: VS269: PASSED +177: VS270: PASSED +177: VS271: PASSED +177: VS272: PASSED +177: VS273: PASSED +177: VS274: PASSED +177: VS275: PASSED +177: VS276: PASSED +177: VS277: PASSED +177: VS278: PASSED +177: VS279: PASSED +177: VS280: PASSED +177: VS281: PASSED +177: VS282: PASSED +177: VS283: PASSED +177: VS284: PASSED +177: VS285: PASSED +177: VS286: PASSED +177: VS287: PASSED +177: VS288: PASSED +177: VS289: PASSED +177: VS290: PASSED +177: VS291: PASSED +177: VS292: PASSED +177: VS293: PASSED +177: VS294: PASSED +177: VS295: PASSED +177: VS296: PASSED +177: VS297: PASSED +177: VS298: PASSED +177: VS299: PASSED +177: VS300: PASSED +177: Check finished: 0 molecules failed. +177: Failed: +220/236 Test #177: pyCIPLabelsValidation .................. Passed 29.62 sec +29: Checking against /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +29: All 191 tests passed +152: .............[14:18:14] Molecule does not have explicit Hs. Consider calling AddHs() +152: [14:18:14] Molecule does not have explicit Hs. Consider calling AddHs() +152: [14:18:14] Molecule does not have explicit Hs. Consider calling AddHs() +152: [14:18:14] Molecule does not have explicit Hs. Consider calling AddHs() +152: [14:18:14] Molecule does not have explicit Hs. Consider calling AddHs() +152: [14:18:14] Molecule does not have explicit Hs. Consider calling AddHs() +152: [14:18:14] Molecule does not have explicit Hs. Consider calling AddHs() +152: [14:18:14] Molecule does not have explicit Hs. Consider calling AddHs() +152: [14:18:14] Molecule does not have explicit Hs. Consider calling AddHs() +152: [14:18:14] Molecule does not have explicit Hs. Consider calling AddHs() +152: [14:18:14] Molecule does not have explicit Hs. Consider calling AddHs() +29: +29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.smi... +185: ......[14:18:15] +185: +185: **** +185: Pre-condition Violation +185: RingInfo not initialized +185: Violation occurred on line 52 in file ./Code/GraphMol/RingInfo.cpp +185: Failed Expression: df_init +185: ---------- +185: Stacktrace: +185: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +185: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +185: 2# RDKit::RingInfo::numAtomRings(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +185: 3# RDKit::AtomRingQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 +185: 4# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +185: 5# RDKit::atomCompat(RDKit::Atom const*, RDKit::Atom const*, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +185: 6# boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::IsFeasiblePair(unsigned int, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +185: 7# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +185: 8# bool boost::vf2_all, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor, std::vector, std::allocator > >, std::allocator, std::allocator > > > > >(boost::adjacency_list const&, boost::adjacency_list const&, RDKit::detail::AtomLabelFunctor&, RDKit::detail::BondLabelFunctor&, RDKit::MolMatchFinalCheckFunctor&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +185: 9# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +185: 10# bool RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >&, bool, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +185: 11# bool RDKit::HasSubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, bool, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +185: 12# 0x00007F865DA5D1D5 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +185: 13# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +185: 14# 0x00007F865FE5062C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +185: 15# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +185: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so +185: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so +185: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so +185: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +185: 20# 0x00007F865D9B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +185: 21# 0x00007F865D9B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +185: 22# 0x00007F865D9B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +185: 23# 0x00007F865D9B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +185: 24# 0x00007F865D9B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +185: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so +185: 26# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so +185: 27# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so +185: 28# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so +185: 29# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +185: 30# 0x00007F865FE4D3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +185: 31# _PyObject_MakeTpCall in /usr/bin/python3 +185: 32# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 33# 0x00000000005CD3C9 in /usr/bin/python3 +185: 34# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 35# 0x0000000000690C6F in /usr/bin/python3 +185: 36# 0x000000000062D590 in /usr/bin/python3 +185: 37# _PyObject_MakeTpCall in /usr/bin/python3 +185: 38# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 39# 0x00000000005CD3C9 in /usr/bin/python3 +185: 40# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 41# 0x0000000000690C6F in /usr/bin/python3 +185: 42# 0x000000000062D590 in /usr/bin/python3 +185: 43# _PyObject_MakeTpCall in /usr/bin/python3 +185: 44# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 45# 0x00000000005CD3C9 in /usr/bin/python3 +185: 46# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 47# 0x0000000000690C6F in /usr/bin/python3 +185: 48# 0x000000000062D590 in /usr/bin/python3 +185: 49# _PyObject_MakeTpCall in /usr/bin/python3 +185: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 51# 0x00000000005A090C in /usr/bin/python3 +185: 52# _PyObject_MakeTpCall in /usr/bin/python3 +185: 53# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 54# PyEval_EvalCode in /usr/bin/python3 +185: 55# 0x00000000006AB8D1 in /usr/bin/python3 +185: 56# 0x00000000006A899C in /usr/bin/python3 +185: 57# 0x00000000006B9943 in /usr/bin/python3 +185: 58# 0x00000000006B93E3 in /usr/bin/python3 +185: 59# 0x00000000006B921E in /usr/bin/python3 +185: 60# Py_RunMain in /usr/bin/python3 +185: 61# Py_BytesMain in /usr/bin/python3 +185: 62# 0x00007F8660793CA8 in /lib/x86_64-linux-gnu/libc.so.6 +185: 63# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +185: 64# _start in /usr/bin/python3 +185: ---------- +185: **** +185: +185: [14:18:15] +185: +185: **** +185: Pre-condition Violation +185: RingInfo not initialized +185: Violation occurred on line 129 in file ./Code/GraphMol/RingInfo.cpp +185: Failed Expression: df_init +185: ---------- +185: Stacktrace: +185: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +185: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +185: 2# RDKit::RingInfo::numBondRings(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +185: 3# 0x00007F865D4E6800 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +185: 4# Queries::EqualityQuery::Match(RDKit::Bond const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +185: 5# RDKit::bondCompat(RDKit::Bond const*, RDKit::Bond const*, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +185: 6# boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::IsFeasiblePair(unsigned int, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +185: 7# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +185: 8# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +185: 9# bool boost::vf2_all, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor, std::vector, std::allocator > >, std::allocator, std::allocator > > > > >(boost::adjacency_list const&, boost::adjacency_list const&, RDKit::detail::AtomLabelFunctor&, RDKit::detail::BondLabelFunctor&, RDKit::MolMatchFinalCheckFunctor&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +185: 10# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +185: 11# bool RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >&, bool, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +185: 12# bool RDKit::HasSubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, bool, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +185: 13# 0x00007F865DA5D1D5 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +185: 14# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +185: 15# 0x00007F865FE5062C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +185: 16# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +185: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so +185: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so +185: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so +185: 20# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +185: 21# 0x00007F865D9B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +185: 22# 0x00007F865D9B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +185: 23# 0x00007F865D9B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +185: 24# 0x00007F865D9B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +185: 25# 0x00007F865D9B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +185: 26# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so +185: 27# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so +185: 28# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so +185: 29# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so +185: 30# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +185: 31# 0x00007F865FE4D3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +185: 32# _PyObject_MakeTpCall in /usr/bin/python3 +185: 33# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 34# 0x00000000005CD3C9 in /usr/bin/python3 +185: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 36# 0x0000000000690C6F in /usr/bin/python3 +185: 37# 0x000000000062D590 in /usr/bin/python3 +185: 38# _PyObject_MakeTpCall in /usr/bin/python3 +185: 39# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 40# 0x00000000005CD3C9 in /usr/bin/python3 +185: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 42# 0x0000000000690C6F in /usr/bin/python3 +185: 43# 0x000000000062D590 in /usr/bin/python3 +185: 44# _PyObject_MakeTpCall in /usr/bin/python3 +185: 45# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 46# 0x00000000005CD3C9 in /usr/bin/python3 +185: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 48# 0x0000000000690C6F in /usr/bin/python3 +185: 49# 0x000000000062D590 in /usr/bin/python3 +185: 50# _PyObject_MakeTpCall in /usr/bin/python3 +185: 51# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 52# 0x00000000005A090C in /usr/bin/python3 +185: 53# _PyObject_MakeTpCall in /usr/bin/python3 +185: 54# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 55# PyEval_EvalCode in /usr/bin/python3 +185: 56# 0x00000000006AB8D1 in /usr/bin/python3 +185: 57# 0x00000000006A899C in /usr/bin/python3 +185: 58# 0x00000000006B9943 in /usr/bin/python3 +185: 59# 0x00000000006B93E3 in /usr/bin/python3 +185: 60# 0x00000000006B921E in /usr/bin/python3 +185: 61# Py_RunMain in /usr/bin/python3 +185: 62# Py_BytesMain in /usr/bin/python3 +185: 63# 0x00007F8660793CA8 in /lib/x86_64-linux-gnu/libc.so.6 +185: 64# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +185: 65# _start in /usr/bin/python3 +185: ---------- +185: **** +185: +152: ...[14:18:17] Molecule does not have explicit Hs. Consider calling AddHs() +152: [14:18:17] Molecule does not have explicit Hs. Consider calling AddHs() +152: [14:18:17] Molecule does not have explicit Hs. Consider calling AddHs() +152: [14:18:17] Molecule does not have explicit Hs. Consider calling AddHs() +152: [14:18:17] Molecule does not have explicit Hs. Consider calling AddHs() +152: ... +152: ---------------------------------------------------------------------- +152: Ran 19 tests in 35.503s +152: +152: OK +152: Testing MolAlign Wrappers +221/236 Test #152: pyMolAlign ............................. Passed 36.48 sec 163: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds 163: MCS MatchStereo true : [#6]-[#6]-[#6] 3 atoms, 2 bonds 163: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds 163: MCS MatchStereo true : [#6]-[#6]-[#6] 3 atoms, 2 bonds 163: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds 163: MCS MatchStereo true : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds -163: TOTAL Time elapsed 20.11 seconds -225/236 Test #163: testFMCS ............................... Passed 20.18 sec -173: [17:55:40] Complex queries can be slow. -173: [17:55:40] Complex queries can be slow. -173: [17:55:41] Complex queries can be slow. -173: [17:55:41] Complex queries can be slow. -173: [17:55:41] Complex queries can be slow. -173: [17:55:41] Complex queries can be slow. -173: [17:55:41] Complex queries can be slow. -173: [17:55:41] Complex queries can be slow. +163: TOTAL Time elapsed 38.03 seconds +222/236 Test #163: testFMCS ............................... Passed 38.15 sec +173: [14:18:20] Complex queries can be slow. +173: [14:18:20] Complex queries can be slow. +173: [14:18:20] Complex queries can be slow. +173: [14:18:20] Complex queries can be slow. +173: [14:18:20] Complex queries can be slow. +173: [14:18:20] Complex queries can be slow. +173: [14:18:20] Complex queries can be slow. +173: [14:18:21] Complex queries can be slow. +173: [14:18:21] Complex queries can be slow. +173: [14:18:21] Complex queries can be slow. +173: [14:18:21] Complex queries can be slow. +173: [14:18:22] Complex queries can be slow. +173: [14:18:22] Complex queries can be slow. +173: [14:18:22] Complex queries can be slow. +173: [14:18:23] Complex queries can be slow. +173: [14:18:23] Complex queries can be slow. +173: [14:18:24] Complex queries can be slow. +173: [14:18:25] Complex queries can be slow. +210: [14:18:25] Explicit valence for atom # 0 Br, 1, is greater than permitted +210: =============================================================================== +210: All tests passed (38344 assertions in 51 test cases) +210: +223/236 Test #210: molStandardizeCatchTest ................ Passed 37.08 sec +173: [14:18:25] Complex queries can be slow. +173: =============================================================================== +173: All tests passed (121 assertions in 17 test cases) +173: +224/236 Test #173: testSynthonSpaceSubstructureSearch ..... Passed 43.64 sec 150: --------------------------------- 150: test O3A multithreading bug 150: @@ -34839,49 +34857,72 @@ 150: testCrippenO3A multithreading 150: 150: generating reference data -173: [17:55:41] Complex queries can be slow. -173: [17:55:41] Complex queries can be slow. -173: =============================================================================== -173: All tests passed (121 assertions in 17 test cases) -173: -226/236 Test #173: testSynthonSpaceSubstructureSearch ..... Passed 20.95 sec 150: processing 150: launch :0 150: launch :1 150: launch :2 150: launch :3 -210: [17:55:44] Explicit valence for atom # 0 Br, 1, is greater than permitted -210: =============================================================================== -210: All tests passed (38344 assertions in 51 test cases) -210: -227/236 Test #210: molStandardizeCatchTest ................ Passed 20.43 sec -148: .........[17:55:45] Molecule does not have explicit Hs. Consider calling AddHs() -148: .[17:55:45] Molecule does not have explicit Hs. Consider calling AddHs() -148: [17:55:45] Molecule does not have explicit Hs. Consider calling AddHs() -148: [17:55:45] Molecule does not have explicit Hs. Consider calling AddHs() -148: [17:55:45] Molecule does not have explicit Hs. Consider calling AddHs() -148: [17:55:45] Molecule does not have explicit Hs. Consider calling AddHs() -148: [17:55:45] Molecule does not have explicit Hs. Consider calling AddHs() -148: [17:55:45] Molecule does not have explicit Hs. Consider calling AddHs() -148: [17:55:45] Molecule does not have explicit Hs. Consider calling AddHs() -148: [17:55:45] Molecule does not have explicit Hs. Consider calling AddHs() -148: [17:55:45] Molecule does not have explicit Hs. Consider calling AddHs() -148: .[17:55:45] Molecule does not have explicit Hs. Consider calling AddHs() -148: [17:55:45] Molecule does not have explicit Hs. Consider calling AddHs() -148: [17:55:45] Molecule does not have explicit Hs. Consider calling AddHs() -148: [17:55:45] Molecule does not have explicit Hs. Consider calling AddHs() -148: [17:55:45] Molecule does not have explicit Hs. Consider calling AddHs() -148: [17:55:45] Molecule does not have explicit Hs. Consider calling AddHs() -148: [17:55:45] Molecule does not have explicit Hs. Consider calling AddHs() -148: [17:55:45] Molecule does not have explicit Hs. Consider calling AddHs() -148: [17:55:45] Molecule does not have explicit Hs. Consider calling AddHs() -148: [17:55:45] Molecule does not have explicit Hs. Consider calling AddHs() +29: Checking against /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +29: All 191 tests passed +29: done +29: ------------------------------------- +29: Unit tests for all MMFF constraint terms. +29: 10.0003 +29: done +29: ------------------------------------- +29: Unit test for MMFF TorsionConstraint close to 0 degrees. +29: done +29: ------------------------------------- +29: Unit tests for copying MMFF ForceFields. +29: done +29: ------------------------------------- +29: Unit test for MMFF butane scan. +29: done +225/236 Test #29: testMMFFForceField ..................... Passed 55.87 sec +226/236 Test #199: pyTestThreads .......................... Passed 47.70 sec +148: .........[14:18:36] Molecule does not have explicit Hs. Consider calling AddHs() +148: .[14:18:36] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:18:36] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:18:36] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:18:36] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:18:36] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:18:36] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:18:36] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:18:36] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:18:36] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:18:36] Molecule does not have explicit Hs. Consider calling AddHs() +148: .[14:18:36] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:18:36] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:18:36] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:18:36] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:18:36] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:18:36] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:18:36] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:18:36] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:18:36] Molecule does not have explicit Hs. Consider calling AddHs() +148: [14:18:36] Molecule does not have explicit Hs. Consider calling AddHs() +185: ............. +185: ---------------------------------------------------------------------- +185: Ran 19 tests in 51.861s +185: +185: OK +185: Testing atom rings +185: testing bond rings +185: searching atom rings +185: searching bond rings +185: done +227/236 Test #185: pySubstructLibrary ..................... Passed 53.09 sec 148: ... 148: ---------------------------------------------------------------------- -148: Ran 22 tests in 27.546s +148: Ran 22 tests in 66.485s 148: 148: OK -228/236 Test #148: pyDistGeomHelpers ...................... Passed 28.03 sec +228/236 Test #148: pyDistGeomHelpers ...................... Passed 67.31 sec +150: --------------------------------- +150: test getO3AForProbeConfs +150: +150: *********************************************************** +229/236 Test #150: testO3AAlign ........................... Passed 79.04 sec 236: DbCLI/UnitTestDbCLI.py ............ [100%] 236: 236: =============================== warnings summary =============================== @@ -34890,58 +34931,51 @@ 236: decBase = declarative_base() 236: 236: -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html -236: ======================== 12 passed, 1 warning in 22.56s ======================== -229/236 Test #236: pythonProjectTests ..................... Passed 24.23 sec -150: --------------------------------- -150: test getO3AForProbeConfs -150: -150: *********************************************************** -230/236 Test #150: testO3AAlign ........................... Passed 30.36 sec -5: [17:55:51] Finished: testMultipleTimes() -5: [17:55:51] -5: ----------------------------------------- -231/236 Test #5: testConcurrentQueue .................... Passed 34.22 sec -147: [17:55:53] UFFTYPER: Unrecognized atom type: S_6+6 (0) -147: [17:55:53] UFFTYPER: Warning: hybridization set to SP3 for atom 0 -147: [17:55:53] UFFTYPER: Unrecognized charge state for atom: 0 -146: [17:56:10] done -146: [17:56:10] --------------------------------- -146: [17:56:10] test github issue 256: handling of zero-atom molecules +236: =================== 12 passed, 1 warning in 68.72s (0:01:08) =================== +230/236 Test #236: pythonProjectTests ..................... Passed 69.78 sec +170: [14:19:04] Timed out after 71 seconds. +147: [14:19:11] UFFTYPER: Unrecognized atom type: S_6+6 (0) +147: [14:19:11] UFFTYPER: Warning: hybridization set to SP3 for atom 0 +147: [14:19:11] UFFTYPER: Unrecognized charge state for atom: 0 +146: [14:19:52] done +171: =============================================================================== +171: All tests passed (93 assertions in 5 test cases) +171: +231/236 Test #171: testRascalCluster ...................... Passed 132.99 sec +146: [14:19:52] --------------------------------- +146: [14:19:52] test github issue 256: handling of zero-atom molecules 146: -146: [17:56:10] --------------------------------- -146: [17:56:10] test embedder callback function -146: [17:56:10] --------------------------------- -146: [17:56:10] test multi-threaded multi-conf embedding +146: [14:19:52] --------------------------------- +146: [14:19:52] test embedder callback function +146: [14:19:52] --------------------------------- +146: [14:19:52] test multi-threaded multi-conf embedding 146: -146: [17:56:16] --------------------------------- -146: [17:56:16] test github issue 563: Incorrect ring stereochemistry after embedding +146: [14:20:02] --------------------------------- +146: [14:20:02] test github issue 563: Incorrect ring stereochemistry after embedding 146: 146: CNC[C@H]1CC[C@H](C[NH3+])CC1 -146: [17:56:18] --------------------------------- -146: [17:56:18] test github issue 568: Incorrect stereochemistry after embedding +146: [14:20:08] --------------------------------- +146: [14:20:08] test github issue 568: Incorrect stereochemistry after embedding 146: 146: C1=NC[C@]2(CN3CC[C@@H]2C3)O1 146: O=C(O)[C@@H]1[C@H](C(=O)O)[C@H]2CC[C@@H]1O2 146: O=C(CCc1ccccc1)OC[C@H]1C[C@@H]2O[C@H]1[C@H]1C(=O)OC(=O)[C@H]12 146: Cn1cc(C2=NC[C@]3(CN4CC[C@@H]3C4)O2)c2ccccc21 -171: =============================================================================== -171: All tests passed (93 assertions in 5 test cases) -171: 146: Nc1ncnc2c1ncn2[C@@H]1C=C(CO)[C@@H](O)[C@H]1O -232/236 Test #171: testRascalCluster ...................... Passed 60.97 sec 146: CO[C@H]1[C@@H](N)[C@@H](O)[C@@H](O)[C@H]1O 146: CO[C@@H]1[C@@H](N)[C@@H](O)[C@@H](O)[C@H]1O 146: CCS[C@@H]1[C@@H](N)[C@@H](O)[C@@H](O)[C@H]1O +170: =============================================================================== +170: All tests passed (3590 assertions in 35 test cases) +170: +232/236 Test #170: testRascalMCES ......................... Passed 152.65 sec 146: CCCCC[C@H](O)/C=C/[C@@]1(F)[C@H](O)C[C@H](O)[C@@H]1C/C=C\CCCC(=O)OC 146: CCCCC[C@@H](O)/C=C/[C@@]1(F)[C@H](C/C=C\CCCC(=O)OC)[C@H](O)C[C@@H]1O 146: CNC(=O)Oc1cccc2c1OC[C@@H]1CCN(C)[C@H]21 146: CNC(=O)Oc1ccc2c(c1)[C@@H]1[C@@H](CCN1C)CO2 146: CN1CC[C@H]2COc3c(O)cccc3[C@H]21 146: CC(=O)C[C@@]12CCC[C@H]1[C@@H]1CCC3=CC(=O)CC[C@@H]3[C@H]1CC2 -146: O=C(O)[C@@H]1C[C@H]2C[C@@H](CCc3nn[nH]n3)CC[C@H]2CN1 -146: COc1ccc2c(c1)OC[C@@H](N1CCC(O)(c3ccc(F)cc3)CC1)[C@H]2O -146: Oc1ccc2c(c1)OC[C@@H](N1CCC(Cc3ccccc3)CC1)[C@H]2O -147: [17:56:28] Interrupted, cancelling conformer generation +147: [14:20:21] Interrupted, cancelling conformer generation 147: Atoms: 147: 0 6 C chg: 0 deg: 4 exp: 4 imp: 0 hyb: SP3 chi: CCW nbrs:[9 3 1 6] 147: 1 6 C chg: 0 deg: 4 exp: 4 imp: 0 hyb: SP3 chi: CCW nbrs:[0 13 6 7] @@ -34974,17 +35008,16 @@ 147: 13 7->5 order: 1 147: 14 8->12 order: a conj?: 1 aromatic?: 1 147: 15 11->2 order: 1 stereo: CCW bonds: (9 4 5) conj?: 1 -146: Oc1ccc2c(c1)OC[C@H](N1CCC(O)(c3ccccc3)CC1)[C@@H]2O 147: =============================================================================== 147: All tests passed (12742 assertions in 21 test cases) 147: -233/236 Test #147: distGeomHelpersCatch ................... Passed 68.40 sec +233/236 Test #147: distGeomHelpersCatch ................... Passed 162.27 sec +146: O=C(O)[C@@H]1C[C@H]2C[C@@H](CCc3nn[nH]n3)CC[C@H]2CN1 +146: COc1ccc2c(c1)OC[C@@H](N1CCC(O)(c3ccc(F)cc3)CC1)[C@H]2O +146: Oc1ccc2c(c1)OC[C@@H](N1CCC(Cc3ccccc3)CC1)[C@H]2O +146: Oc1ccc2c(c1)OC[C@H](N1CCC(O)(c3ccccc3)CC1)[C@@H]2O 146: CC(=O)c1ccc2c(c1)[C@@]13CCCC[C@H]1[C@@H](C2)N(CC1CC1)CC3 146: CC(=O)O[C@@H]1CC[C@@H]2CN3CCc4cc5c(cc4[C@@H]3C[C@@H]2C1)OCO5 -170: =============================================================================== -170: All tests passed (3590 assertions in 35 test cases) -170: -234/236 Test #170: testRascalMCES ......................... Passed 70.27 sec 146: COc1cc2c(cc1OC)[C@@H]1C[C@@H]3C[C@H](O)CC[C@@H]3CN1CC2 146: N#C[C@@H]1C[C@@H]2CN3CCc4cc5c(cc4[C@@H]3C[C@@H]2C[C@@H]1O)OCO5 146: COC(=O)[C@@H]1C[C@](C)(C(=O)O)NC(=O)N1 @@ -34993,48 +35026,52 @@ 146: C[C@H](C(N)=O)N1CC[C@@]23CCCC[C@@H]2[C@@H]1Cc1ccc(OCc2cccc(F)c2)cc13 146: CN1C(=O)CC[C@@]2(C)C1=CCc1cc(Cl)ccc12 146: Cc1nc(COc2ccc3c(c2)[C@@H](O)[C@@H](Cc2cccnc2)CO3)ccc1[N+](=O)[O-] -146: [17:56:50] Molecule does not have explicit Hs. Consider calling AddHs() -146: [17:56:43] --------------------------------- -146: [17:56:43] test github issue 696: Bad 1-4 bounds matrix elements in highly constrained system -146: [17:56:43] --------------------------------- -146: [17:56:43] More ChEMBL molecules failing bounds smoothing. -146: [17:56:43] --------------------------------- -146: [17:56:43] ugly conformations can be generated for highly constrained ring systems. -146: [17:56:43] --------------------------------- -146: [17:56:43] test embed parameters structure. -146: [17:56:43] --------------------------------- -146: [17:56:43] test github 1227: Hs being used in RMSD filtering. -146: [17:56:43] --------------------------------- -146: [17:56:43] Failure to embed larger aromatic rings. -146: [17:56:44] --------------------------------- -146: [17:56:44] Deterministic with large random seeds -146: [17:56:49] --------------------------------- -146: [17:56:49] Github #1990: seg fault after RemoveHs -146: [17:56:49] --------------------------------- -146: [17:56:49] Github #2246: Use coordMap when starting embedding from random coords -146: [17:56:50] --------------------------------- -146: [17:56:50] Providing a distance bounds matrix. -146: [17:56:50] --------------------------------- -146: [17:56:50] Disabling fragmentation. -146: [17:56:50] --------------------------------- -146: [17:56:50] Using symmetry in conformation pruning. -146: [17:56:50] --------------------------------- -146: [17:56:50] Force trans amides. -146: [17:56:50] --------------------------------- -146: [17:56:50] test missing Hs warning. -146: [17:56:50] --------------------------------- -146: [17:56:50] basic H bond support. -146: [17:56:50] ******************************************************* -235/236 Test #146: testDistGeomHelpers .................... Passed 89.99 sec -174: Randomness seeded to: 1913649888 +146: [14:20:55] Molecule does not have explicit Hs. Consider calling AddHs() +146: [14:20:45] --------------------------------- +146: [14:20:45] test github issue 696: Bad 1-4 bounds matrix elements in highly constrained system +146: [14:20:45] --------------------------------- +146: [14:20:45] More ChEMBL molecules failing bounds smoothing. +146: [14:20:45] --------------------------------- +146: [14:20:45] ugly conformations can be generated for highly constrained ring systems. +146: [14:20:46] --------------------------------- +146: [14:20:46] test embed parameters structure. +146: [14:20:46] --------------------------------- +146: [14:20:46] test github 1227: Hs being used in RMSD filtering. +146: [14:20:46] --------------------------------- +146: [14:20:46] Failure to embed larger aromatic rings. +146: [14:20:48] --------------------------------- +146: [14:20:48] Deterministic with large random seeds +146: [14:20:52] --------------------------------- +146: [14:20:52] Github #1990: seg fault after RemoveHs +146: [14:20:52] --------------------------------- +146: [14:20:52] Github #2246: Use coordMap when starting embedding from random coords +146: [14:20:55] --------------------------------- +146: [14:20:55] Providing a distance bounds matrix. +146: [14:20:55] --------------------------------- +146: [14:20:55] Disabling fragmentation. +146: [14:20:55] --------------------------------- +146: [14:20:55] Using symmetry in conformation pruning. +146: [14:20:55] --------------------------------- +146: [14:20:55] Force trans amides. +146: [14:20:55] --------------------------------- +146: [14:20:55] test missing Hs warning. +146: [14:20:55] --------------------------------- +146: [14:20:55] basic H bond support. +146: [14:20:55] ******************************************************* +234/236 Test #146: testDistGeomHelpers .................... Passed 195.75 sec +174: Randomness seeded to: 3814782885 174: =============================================================================== 174: All tests passed (28 assertions in 2 test cases) 174: -236/236 Test #174: testSynthonSpaceRascalSearch ........... Passed 105.45 sec +235/236 Test #174: testSynthonSpaceRascalSearch ........... Passed 240.06 sec +5: [14:40:55] Finished: testMultipleTimes() +5: [14:40:55] +5: ----------------------------------------- +236/236 Test #5: testConcurrentQueue .................... Passed 1398.56 sec 100% tests passed, 0 tests failed out of 236 -Total Test time (real) = 109.54 sec +Total Test time (real) = 1399.44 sec make[2]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[1]: Leaving directory '/build/reproducible-path/rdkit-202503.1' create-stamp debian/debhelper-build-stamp @@ -35044,7 +35081,7 @@ debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/rdkit-202503.1' dh_auto_install - cd obj-x86_64-linux-gnu && make -j42 install DESTDIR=/build/reproducible-path/rdkit-202503.1/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-x86_64-linux-gnu && make -j40 install DESTDIR=/build/reproducible-path/rdkit-202503.1/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/rdkit-202503.1 -B/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -35055,1278 +35092,1278 @@ /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/RDRandom.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DistanceGeometry +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DistanceGeometry/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Numerics +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Numerics/__init__.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils/chemdraw.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils/cactvs.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils/listutils.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils/retest.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils/chemdraw_qax.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils/fileutils.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils/chemutils.py +-- Installing: 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/build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MACCSkeys.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/FastSDMolSupplier.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/fmcs --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/fmcs/fmcs --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/fmcs/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/fmcs/fmcs.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/AllChem.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Pharm3D --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Pharm3D/ExcludedVolume.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Pharm3D/EmbedLib.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Pharm3D/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Pharm3D/Pharmacophore.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MCS.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolKey --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolKey/InchiInfo.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolKey/MolKey.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolKey/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Graphs.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolSurf.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/SaltRemover.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Fragments.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Draw --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Draw/IPythonConsole.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Draw/MolDrawing.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Draw/FreeSans.ttf --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Draw/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Draw/SimilarityMaps.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Draw/InteractiveRenderer.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Descriptors.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Recap.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/inchi.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolDb --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolDb/Loader.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolDb/FingerprintUtils.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolDb/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolDb/Loader_sa.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolDb/Loader_orig.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/Stats.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/MLData.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/DataUtils.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/SplitData.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/Transforms.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/FindQuantBounds.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/Quantize.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/files.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/SLT --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/SLT/Risk.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/SLT/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Scoring --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Scoring/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Scoring/Scoring.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Descriptors --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Descriptors/CompoundDescriptors.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Descriptors/MoleculeDescriptors.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Descriptors/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Descriptors/Parser.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Descriptors/Descriptors.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/InfoTheory --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/InfoTheory/entropy.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/InfoTheory/BitRank.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/InfoTheory/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/InfoTheory/BitClusterer.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/MLUtils --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/MLUtils/VoteImg.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/MLUtils/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/MatOps.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/ClusterVis.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/murtagh_test.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/Clusters.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/Resemblance.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/ClusterUtils.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/Murtagh.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/Standardize.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/Butina.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils/fileutils.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Qt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Qt/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Qt/pidQt4.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Qt/pidQt.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Pyart +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Pyart/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Pyart/Fontmapping.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Pyart/pidPyart.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/SVG +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/SVG/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/SVG/pidSVG.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/colors.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/stringformat.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/pagesizes.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/patches +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/patches/Imaging-1.1.1.diff +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/patches/Imaging-1.1-fixplugin-path +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/__init__.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PDF --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PDF/pdfgeom.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PDF/pidPDF.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PDF/pdfgen.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PDF/pdfgeom.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PDF/pdfdoc.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PDF/pdfmetrics.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PDF/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PDF/pidPDF.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PDF/pdfutils.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/ReportLab --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/ReportLab/pidReportLab.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/ReportLab/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/util --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/util/HTMLPiddler.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/util/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PS --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PS/psmetrics.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PS/fontinfo.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PS/latin1MetricsCache.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PS/pidPS.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PS/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/pid.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PDF/pdfmetrics.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/tests -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/tests/pidtest.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/tests/pstests.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/tests/testallps.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/tests/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/SVG --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/SVG/pidSVG.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/SVG/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Pyart --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Pyart/pidPyart.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Pyart/Fontmapping.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Pyart/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/utils.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/stringformat.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/colors.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/__init__.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pidPIL.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/__init__.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-24.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-8.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-10.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-14.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-8.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-24.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-8.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-24.pil -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-18.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-10.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-10.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-14.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-8.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-8.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-10.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-8.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-18.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-24.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-24.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-12.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-12.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-14.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-18.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-14.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-12.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-14.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-8.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-10.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-10.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-18.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-12.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-18.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-10.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/removemedium.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-24.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-24.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-12.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-10.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-24.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-18.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-10.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-12.pil -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-14.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-10.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-12.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-14.pil -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-14.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-8.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-24.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-18.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-8.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-10.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-14.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-8.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-14.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-18.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-10.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-18.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-10.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-24.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-8.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-24.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-18.pil -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-10.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-8.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-24.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-8.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-14.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-18.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-24.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-24.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-10.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-24.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-18.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/metrics.dat +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-8.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-10.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-12.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-14.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-24.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-18.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-24.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-12.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-18.pil -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-12.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-8.pil.1 --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-12.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-12.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-24.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-18.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-8.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-18.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-12.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-14.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-18.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-24.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/metrics.dat --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-18.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-12.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-24.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-24.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-14.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-10.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-8.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-14.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-24.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-14.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-10.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-14.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-8.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-24.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-18.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-12.pil -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-12.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-14.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-12.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-10.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-10.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-12.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-14.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-18.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-8.pil.1 +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-18.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-8.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-14.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-8.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-12.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-8.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-24.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-8.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-8.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-24.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-8.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/removemedium.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-18.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-10.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-14.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-12.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-12.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-14.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-18.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/pagesizes.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Qt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Qt/pidQt.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Qt/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Qt/pidQt4.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-24.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-18.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-10.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-14.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-12.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-8.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-8.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-24.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-18.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-14.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-10.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-14.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-10.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-12.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-10.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pidPIL.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/pid.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/util +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/util/HTMLPiddler.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/util/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/WX +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/WX/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/WX/pidWxDc.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/WX/pidWX.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/examples --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/examples/tkCanvas-with-scrollbars.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/examples/tkCanvasPIL-with-scrollbars.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/examples/formatted-strings.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/patches --- Installing: 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/build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/WX --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/WX/pidWX.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/WX/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/WX/pidWxDc.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/README --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Numerics --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Numerics/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/HierarchyVis.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/VectCollection.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/TopNContainer.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/LazySignature.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/BitUtils.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/BitEnsemble.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/BitEnsembleDb.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/ReportLab +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/ReportLab/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/ReportLab/pidReportLab.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/utils.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PS +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PS/psmetrics.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PS/pidPS.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PS/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PS/fontinfo.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PS/latin1MetricsCache.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Avalon -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Avalon/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ForceField --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ForceField/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/__init__.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/pytest.ini -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/Transform.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/Supply.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/Output.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/Node.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/Supply.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/Transform.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/DbPickleSupplier.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/SDSupply.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/SmartsMolFilter.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/SmilesSupply.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/demo.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/__init__.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/SmartsRemover.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/DbPickleSupplier.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/demo.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/SmilesOutput.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/SmilesDupeFilter.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/DbMolSupply.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/SDSupply.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/SmartsMolFilter.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/SmilesOutput.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/Output.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/Filter.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/RDConfig.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Geometry +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Geometry/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/RDLogger.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Dbase --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Dbase/DbResultSet.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Dbase/DbConnection.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Dbase/__init__.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Dbase/DbInfo.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Dbase/DbModule.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Dbase/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Dbase/DbConnection.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Dbase/DbUtils.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Dbase/DbResultSet.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Dbase/StorageUtils.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Dbase/DbUtils.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/RDConfig.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/SimDivFilters +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/SimDivFilters/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/SimDivFilters/SimilarityPickers.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataManip -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataManip/Metric -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataManip/Metric/__init__.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataManip/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/RDLogger.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MCS.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/PandasPatcher.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolKey +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolKey/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolKey/InchiInfo.py +-- Installing: 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/build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/nbtests +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/nbtests/github4823.ipynb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/nbtests/rdkit-structure-renderer.ipynb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/nbtests/ChEMBL_quinolones.tsv +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Randomize.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/inchi.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Pharm3D +-- Installing: 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/build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/SATIS.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/ChemicalForceFields.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Graphs.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/PandasTools.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/FunctionalGroups.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Fingerprints +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Fingerprints/SimilarityScreener.py +-- Installing: 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/build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Descriptors.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Scaffolds +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Scaffolds/MurckoScaffold.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Scaffolds/ScaffoldNetwork.ipynb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Scaffolds/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/ChemUtils +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/ChemUtils/DescriptorUtilities.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/ChemUtils/BulkTester.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/ChemUtils/TemplateExpand.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/ChemUtils/SDFToCSV.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/ChemUtils/AlignDepict.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/ChemUtils/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Recap.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Descriptors3D.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolStandardize +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolStandardize/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Draw +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Draw/InteractiveRenderer.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Draw/SimilarityMaps.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Draw/FreeSans.ttf +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Draw/IPythonConsole.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Draw/MolDrawing.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Draw/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Features +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Features/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Features/ShowFeats.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Features/FeatDirUtilsRD.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/EState +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/EState/Fingerprinter.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/EState/EState_VSA.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/EState/AtomTypes.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/EState/EState.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/EState/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Fraggle +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Fraggle/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Fraggle/FraggleSim.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/RegistrationHash.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/FeatMaps +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/FeatMaps/FeatMapPoint.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/FeatMaps/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/FeatMaps/FeatMaps.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/FeatMaps/FeatMapParser.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/FeatMaps/FeatMapUtils.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/PyMol.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolSurf.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/FragmentMatcher.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/ShowMols.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Suppliers +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Suppliers/DbMolSupplier.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Suppliers/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Suppliers/MolSupplier.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Fragments.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/ReducedGraphs.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/TemplateAlign.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/GraphDescriptors.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/FragmentCatalog.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/AtomPairs +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/AtomPairs/Sheridan.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/AtomPairs/Torsions.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/AtomPairs/Utils.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/AtomPairs/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/AtomPairs/Pairs.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Lipinski.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/FeatFinderCLI.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolCatalog.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/SaltRemover.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/DSViewer.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Pharm2D +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Pharm2D/Utils.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Pharm2D/Matcher.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Pharm2D/SigFactory.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Pharm2D/Generate.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Pharm2D/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Pharm2D/Gobbi_Pharm2D.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Pharm2D/LazyGenerator.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/QED.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/fmcs +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/fmcs/fmcs.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/fmcs/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/fmcs/fmcs +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolDb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolDb/FingerprintUtils.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolDb/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolDb/Loader_sa.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolDb/Loader.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolDb/Loader_orig.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Subshape +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Subshape/demoCombined.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Subshape/BuilderUtils.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Subshape/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Subshape/SubshapeObjects.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Subshape/SubshapeAligner.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Subshape/SubshapeBuilder.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/BRICS.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/FastSDMolSupplier.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/ChemicalFeatures.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/SpacialScore.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/AllChem.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Crippen.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ForceField +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ForceField/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/VectCollection.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/BitUtils.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/LazySignature.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/TopNContainer.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/BitEnsembleDb.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/HierarchyVis.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/BitEnsemble.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/RDRandom.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/TestRunner.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/Murtagh.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/ClusterUtils.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/Butina.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/ClusterVis.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/Standardize.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/murtagh_test.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/Resemblance.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/Clusters.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/MLUtils +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/MLUtils/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/MLUtils/VoteImg.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/MatOps.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Scoring +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Scoring/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Scoring/Scoring.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/SLT +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/SLT/Risk.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/SLT/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/InfoTheory +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/InfoTheory/BitRank.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/InfoTheory/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/InfoTheory/BitClusterer.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/InfoTheory/entropy.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/files.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Descriptors +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Descriptors/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Descriptors/Descriptors.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Descriptors/CompoundDescriptors.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Descriptors/MoleculeDescriptors.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Descriptors/Parser.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/Transforms.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/Quantize.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/FindQuantBounds.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/SplitData.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/MLData.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/DataUtils.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/Stats.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/conftest.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/SimDivFilters --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/SimDivFilters/SimilarityPickers.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/SimDivFilters/__init__.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/RDTests.sqlt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/rddata.sql +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Functional_Group_Hierarchy.txt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/FragmentDescriptors.csv +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/struchk +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/struchk/checkfgs.chk +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/struchk/checkfgs.trn +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/struchk/checkfgs.opt -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/DTDs -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/DTDs/RD_Model.dtd --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/DTDs/RD_Dataset.dtd -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/DTDs/validate.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/DTDs/RD_Dataset.dtd -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/FunctionalGroups.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Functional_Group_Hierarchy.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/RDData.sqlt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/NCI --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/NCI/first_5K.smi --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/NCI/first_5k.tpsa.csv --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/NCI/first_200.tpsa.csv --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/NCI/first_200.props.sdf --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Fonts --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Fonts/Amadeus.ttf --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Fonts/telex_font_license.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Fonts/amadeus_font_license.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Fonts/roboto_regular_license.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Fonts/font_dumper.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Fonts/Telex-Regular.ttf --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/FragmentDescriptors.csv -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/SmartsLib +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/SmartsLib/RLewis_smarts.txt -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests/fps.1000.counts.pkl.gz -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests/mols.1000.pkl.gz -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests/bench2.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests/fps.1000.counts.pkl.gz -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/SmartsLib/patty_rules.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/SmartsLib/RLewis_smarts.txt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Salts.txt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/BaseFeatures.fdef +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Crippen.txt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/NCI +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/NCI/first_200.props.sdf +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/NCI/first_5k.tpsa.csv +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/NCI/first_5K.smi +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/NCI/first_200.tpsa.csv +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/RDData.sqlt -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Pains --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Pains/README.md -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Pains/test_data -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Pains/test_data/wehi_mols.csv --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Pains/test_data/test_set3.txt -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Pains/test_data/run_tests.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Pains/test_data/test_set3.txt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Pains/README.md -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Pains/wehi_pains.csv --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/rddata.sql --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Salts.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/BaseFeatures.fdef --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/struchk --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/struchk/checkfgs.chk --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/struchk/checkfgs.opt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/struchk/checkfgs.trn --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/RDTests.sqlt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Crippen.txt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Fonts +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Fonts/font_dumper.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Fonts/Amadeus.ttf +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Fonts/amadeus_font_license.txt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Fonts/telex_font_license.txt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Fonts/Telex-Regular.ttf +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Fonts/roboto_regular_license.txt -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Analysis --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/LeadLikeT80_CorrMat.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/FragmentLikeT80_Correlation.csv --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/DrugLikeT80_CorrMat.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/DrugLikeT80_Correlation.csv --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/FragmentLikeT80_CorrMat.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/LeadLikeT80_Correlation.csv --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/README --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Analysis/ForceField --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Analysis/ForceField/ForceFieldTerms.new.odt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Analysis/ForceField/UFF Parameters.ods +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Images +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Images/logo_plain.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Images/logo_plain.inkscape.svg +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Images/logo.inkscape.svg +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Images/logo.lrg.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Images/logo.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Images/wiki +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Images/wiki/morganfp_atomenv1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Images/logo.ai -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/RDKit_cookbook_jp.rst --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/index.rst --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/An_overview_of_the_RDKit_jp.rst --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/The_RDKit_Book_jp.rst --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/Getting_Started_with_RDKit_in_Python_jp.rst --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/Supplementary_Text_jp.rst --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/introduction_jp.rst +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/conf.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/The_RDKit_database_cartridge_jp.rst -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/Makefile --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/conf.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/Backwards_incompatible_changes_jp.rst +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/Getting_Started_with_RDKit_in_Python_jp.rst -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_50.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_57.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_33.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_54.png -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_38.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_26.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_37.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_17.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_49.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_41.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_7.png -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_20.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_9.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_46.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_6.png -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_19.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_59.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_55.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_5.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_15.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_28.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_35.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_8.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_45.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_2.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_54.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_44.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_46.png -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_11.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_50.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_23.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_39.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_18.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_30.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_10.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_45.png -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_3.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_52.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_60.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_42.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_40.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_12.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_48.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_5.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_35.png -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_61.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_34.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_58.png --- Installing: 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--- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_36.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_25.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_48.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_57.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_10.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_24.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_39.png +-- Installing: 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Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_36.png -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_27.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_37.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_24.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_62.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_25.png -- Installing: 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+-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_49.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_42.png -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_4.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_47.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_34.png -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_21.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_22.png --- Installing: 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/build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_52.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_47.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_59.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_41.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_60.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_32.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_31.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_8.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_9.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_40.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_7.png -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/terminology_jp.rst -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/Installation_jp.rst --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Notebooks --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-example-lactam.ipynb --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Notebooks/MolStandardize.ipynb --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-GA.ipynb --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-DummyCores.ipynb --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Notebooks/FingerprintGenerators.ipynb --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Notebooks/compounds.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-RingSubstitution.ipynb --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-GenericCores.ipynb --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-Tests.ipynb --- Installing: 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/build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/An_overview_of_the_RDKit_jp.rst -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Code --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Code/EnhancedStereo.md --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Code/Chem --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Code/Chem/FragmentCatalogs.html --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Code/Chem/Pharm2D.signatures.ai --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Code/Chem/Pharm2D.triangles.ai --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Code/Chem/Pharm2D.triangles.jpg --- Installing: 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/build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_trans_expand.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Code/EnhancedStereo.md +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Code/CIPLabeling.md +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Code/Chem +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Code/Chem/Pharm2D.triangles.jpg +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Code/Chem/Pharm2D.signatures.ai +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Code/Chem/Pharm2D.signatures.jpg +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Code/Chem/FragmentCatalogs.html +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Code/Chem/Pharm2D.triangles.ai +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Code/SGroups.md +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Code/gsocGeneralFileReader.md -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/RD.css +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Analysis +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Analysis/ForceField +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Analysis/ForceField/ForceFieldTerms.new.odt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Analysis/ForceField/UFF Parameters.ods +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/LeadLikeT80_CorrMat.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/FragmentLikeT80_CorrMat.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/LeadLikeT80_Correlation.csv +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/DrugLikeT80_Correlation.csv +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/DrugLikeT80_CorrMat.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/README +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/FragmentLikeT80_Correlation.csv +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Notebooks +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-GenericCores.ipynb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Notebooks/FingerprintGenerators.ipynb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Notebooks/MolStandardize.ipynb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-MutipleCores.ipynb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-RingSubstitution.ipynb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-example-lactam.ipynb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-Tests.ipynb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-StereoChemTest.ipynb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-DummyCores.ipynb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Notebooks/compounds.txt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-GA.ipynb -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/api-docs.rst +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/GettingStartedInPython.rst +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/BackwardsIncompatibleChanges.md +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/conf.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im4.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_19_im0.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/cdk2_molgrid_aligned.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_2_im1.png +-- Installing: 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/build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_annotation_1.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_34_im0.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_15_im0.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_21_im0.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_29_im0.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/mcs_example_6.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/mfp2_bit872.svg --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_7.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/rdkit_fork_clone.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_6_im2.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/pull_req1.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molE.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/reaction1_highlight.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_labels_2.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/atrop_representation2.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/rdk_bit1553_2.svg --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im3.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_33_im2.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_35_im0.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_33_im0.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_6.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_17_im0.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im6.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_1_im0.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/query_atoms.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_2_im0.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_13_im0.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/atrop_example2.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/similarity_map_fp1.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/atrop_example5.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im0.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/ary_group.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_1.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im5.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/atrop_example3.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_15_im1.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_21_im1.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_0.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_sp2.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_39_im0.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_34_im1.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molA.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/atrop_example4.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_3_im0.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/parastereo_2.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_17_im1.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/Cc1ccccc1.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_30_im1.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_37_im2.svg --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_20_im1.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/stereo_annotation.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/mcs_example_1.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molF.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molB.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_23_im0.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_6_im0.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_37_im0.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_10.jpg --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_21_im3.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/similarity_map_fp2.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molG.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/mcs_example_5.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_1_im2.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_labels_1.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_2_im1.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im2.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/query_bonds.2.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_21_im2.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_22_im1.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_12.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/mol_metadata1.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_labels_3.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molD.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_oh1.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im1.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_21_im4.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im4.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_13_im1.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_sp3.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_21_im5.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molC.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_highlights_2.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_0_im1.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_34_im2.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_28_im1.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_5.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/atrop_representation1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/data +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/data/chiral.mol +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/data/input.mol +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/data/bzr.smi +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/data/5ht3ligs.sdf +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/data/solubility.test.sdf +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/data/README.md +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/data/cdk2.sdf +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/data/test_multi_colours.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/data/AmideBond.rxn +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/data/MinimalFeatures.fdef +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/data/invalid.mol +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/data/solubility.train.sdf +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/data/actives_5ht3.sdf.gz +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/data/bzr.sdf +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/data/s1p_chembldoc89753.txt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/data/actives_5ht3.sdf +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/Overview.md -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/ChiralPairs --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/ChiralPairs/README.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/ChiralPairs/ChiralDescriptors.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Glare --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Glare/glare.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Glare/README.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment/utils.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment/README.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment/identifyReactants.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/mol_transform.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/README.txt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/indexing.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/rfrag.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/create_mmp_db.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/search_mmp_db.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/cansmirk.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_trans_smarts.txt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_sym.csv +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_trans_output.txt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_maxratio.csv +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_fragmented.txt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_trans.txt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_smirks_mol_trans.txt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_smi.txt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mol_trans_output.txt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_smiles_mol_trans.smi +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_maxheavy.csv +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_sym_maxheavy.csv +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/simple.smi +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_default.csv +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_subs_smarts.txt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_subs.txt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_smi_output.txt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_smirks.txt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_transfroms.txt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_cansmirks.txt +-- Installing: 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/build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Fastcluster --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/testdata --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/testdata/sdf2smi.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/testdata/converted.smi --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/testdata/cdk2.sdf --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/README.md --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/clustered_parse.tsv -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/fastcluster.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/fp.tsv -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/clustered.tsv +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/README.md -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/centroid.tsv --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/fp.tsv +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/clustered_parse.tsv +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/testdata +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/testdata/sdf2smi.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/testdata/cdk2.sdf +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/testdata/converted.smi -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/cdk2.smi --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/test_rfrag.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/cansmirk.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_sym_maxheavy.csv --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_subs_output.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_smi_output.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample.smi --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_sym.csv --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mol_trans_output.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_cansmirks.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_maxheavy.csv --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_default.csv --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_smirks_mol_trans.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_trans_smarts_output.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_trans_output.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_maxratio.csv --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_subs_smarts.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_fragmented.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_smiles_mol_trans.smi --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_trans.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_transfroms.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_smirks.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_trans_smarts.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_smi.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_subs.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/simple.smi --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_subs_smart_output.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/indexing.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/search_mmp_db.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/README.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/rfrag.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/mol_transform.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/create_mmp_db.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/SA_Score +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/SA_Score/build_sascore_db.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/SA_Score/sascorer.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/SA_Score/fpscores.pkl.gz +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/SA_Score/data +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/SA_Score/data/zim.100.txt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/SA_Score/README +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/SA_Score/UnitTestSAScore.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/IFG +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/IFG/ifg.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/IFG/README +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/PBF +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/PBF/testData +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/PBF/testData/egfr.sdf +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/PBF/testData/egfr.out +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/PBF/Makefile +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/PBF/demo.cpp +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/PBF/PBFRDKit.h +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/PBF/PBFRDKit.cpp +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/PBF/README +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/PBF/pbf.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/LEF +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/LEF/README.txt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/LEF/CreateFps.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/LEF/DistancePredict.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/LEF/AddLabels.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/LEF/ClusterFps.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/LEF/DistancePlot.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/NP_Score +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/NP_Score/npscorer.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/NP_Score/publicnp.model.gz +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/NP_Score/README +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment/README.txt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment/identifyReactants.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment/utils.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/Examples_CalcLigRMSD.ipynb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/README.md +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/1C9.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/AKI.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/N15.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/5dpv_complex.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/BEG.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/JVE.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/6c83_complex.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/4i24_1C9.pdb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_SKE_pH74_netcharge1.pdb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_3w2p_1C9_pH74_netcharge1.pdb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_JVE_pH74_netcharge1.pdb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/SKE_renamed.pdb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/aurka_protein_2c6e.pdb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/3m11_AKI.pdb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/4i23_1C9.pdb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/5dpv.pdb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/1d4i_BEG.pdb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/SKE_crystal_aligned_1.pdb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_ACP_pH74_netcharge1.pdb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/crystal_aligned.pdb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_N15_pH74_netcharge1.pdb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/6c83.pdb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/ACP_renamed.pdb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/AKI_renamed.pdb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/BEG_test.pdb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/lig_crystal_aligned.pdb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/JVE_renamed.pdb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/ACP_crystal_aligned_1.pdb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/1C9_renamed.pdb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/5dt0.pdb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/N15_renamed.pdb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/3w2c_N15.pdb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_AKI_pH74_netcharge1.pdb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/ACP_crystal_aligned_2.pdb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/4uzh_JVE.pdb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/CalcLigRMSD.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/ChiralPairs +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/ChiralPairs/README.txt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/ChiralPairs/ChiralDescriptors.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/ConformerParser -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/test.cpp +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/ConformerParser.h +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/ConformerParser.cpp -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/CMakeLists.txt -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/Wrap --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/Wrap/CMakeLists.txt -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/Wrap/testConformerParser.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/Wrap/CMakeLists.txt -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/Wrap/rdConformerParser.cpp --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/ConformerParser.h --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/ConformerParser.cpp --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/FreeWilson --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/requirements.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/data --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/data/CHEMBL2321810.smi --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/data/CHEMBL2321810_act.csv --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/data/CHEMBL2321810_scaffold.mol --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/README.md --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/test --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/test/test_freewilson.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/pytest.ini --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/freewilson.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/setup.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CMakeLists.txt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/SubstructureFilter_HitTriaging_wPubChemExamples.csv +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/README.md +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/assignSubstructureFilters.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/FilterSet_NIBR2019_wPubChemExamples.html +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/examples +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/examples/chembl24_structs_randomtestSample_100_out.csv +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/examples/chembl24_structs_randomtestSample_100.csv +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/filterExamples.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/pzc +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/pzc/p_con.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/pzc/readme.md +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/pzc/p_con.html +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/AtomAtomSimilarity +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/AtomAtomSimilarity/AtomAtomPathSimilarity.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Glare +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Glare/README.txt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Glare/glare.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/.pytest_cache --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/.pytest_cache/README.md -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/.pytest_cache/.gitignore +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/.pytest_cache/README.md -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/.pytest_cache/CACHEDIR.TAG -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/.pytest_cache/v -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/.pytest_cache/v/cache -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/.pytest_cache/v/cache/stepwise -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/.pytest_cache/v/cache/nodeids +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/pytest.ini -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/DbCLI -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr_q1.mol -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr.smi --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr.2.smi -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/pubchem.200.sdf --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr_q1.mol -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr/Fingerprints.sqlt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr/loadErrors.txt -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr/Compounds.sqlt -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr/Descriptors.sqlt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr/loadErrors.txt -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr/AtomPairs.sqlt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr.sdf -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/README +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr.sdf +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr.2.smi -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/DbCLI/__pycache__ -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/DbCLI/__pycache__/CreateDb.cpython-313.pyc -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/DbCLI/__pycache__/UnitTestDbCLI.cpython-313-pytest-8.3.5.pyc -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/DbCLI/__pycache__/SearchDb.cpython-313.pyc --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/DbCLI/SearchDb.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/DbCLI/CreateDb.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/DbCLI/UnitTestDbCLI.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/DbCLI/moe_like.dsc --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/pytest.ini +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/DbCLI/UnitTestDbCLI.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/DbCLI/SearchDb.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Scripts --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Scripts/FeatFinderCLI.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Scripts/create_deb_packages.sh +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Scripts/PythonFormat.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Scripts/test.sh -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Scripts/README.md --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Scripts/create_deb_packages.sh -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Scripts/patch_rdkit_docstrings --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Scripts/patch_rdkit_docstrings/__main__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Scripts/patch_rdkit_docstrings/clang_worker.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Scripts/patch_rdkit_docstrings/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Scripts/patch_rdkit_docstrings/clang_worker.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Scripts/patch_rdkit_docstrings/__main__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Scripts/FeatFinderCLI.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Scripts/gen_rdkit_stubs --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Scripts/gen_rdkit_stubs/__main__.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Scripts/gen_rdkit_stubs/worker.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Scripts/gen_rdkit_stubs/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Scripts/PythonFormat.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Scripts/gen_rdkit_stubs/__main__.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/README.md -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/license.txt -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitRDInchiLib.so.1.2025.03.1 @@ -36372,12 +36409,12 @@ -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/RDGeneral/BetterEnums.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/RDGeneral/enum.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/RDGeneral/hash --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/RDGeneral/hash/hash.hpp -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/RDGeneral/hash/hash_fwd.hpp -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/RDGeneral/hash/extensions.hpp -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/RDGeneral/hash/detail -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/RDGeneral/hash/detail/hash_float.hpp -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/RDGeneral/hash/detail/float_functions.hpp +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/RDGeneral/hash/hash.hpp -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitRDBoost.so.1.2025.03.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitRDBoost.so.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitRDBoost.so @@ -36998,7 +37035,10 @@ dh_python3 -ppython3-rdkit I: dh_python3 fs:421: renaming rdBase.so to rdBase.cpython-313-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming DistGeom.so to DistGeom.cpython-313-x86_64-linux-gnu.so +I: dh_python3 fs:421: renaming rdAlignment.so to rdAlignment.cpython-313-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdGeometry.so to rdGeometry.cpython-313-x86_64-linux-gnu.so +I: dh_python3 fs:421: renaming rdSimDivPickers.so to rdSimDivPickers.cpython-313-x86_64-linux-gnu.so +I: dh_python3 fs:421: renaming rdMetricMatrixCalc.so to rdMetricMatrixCalc.cpython-313-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdAbbreviations.so to rdAbbreviations.cpython-313-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdCIPLabeler.so to rdCIPLabeler.cpython-313-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdChemReactions.so to rdChemReactions.cpython-313-x86_64-linux-gnu.so @@ -37043,14 +37083,11 @@ I: dh_python3 fs:421: renaming rdScaffoldNetwork.so to rdScaffoldNetwork.cpython-313-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdMolStandardize.so to rdMolStandardize.cpython-313-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdMolDraw2D.so to rdMolDraw2D.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming cQuantize.so to cQuantize.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdInfoTheory.so to rdInfoTheory.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming Clustering.so to Clustering.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdAlignment.so to rdAlignment.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming cDataStructs.so to cDataStructs.cpython-313-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdForceField.so to rdForceField.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdMetricMatrixCalc.so to rdMetricMatrixCalc.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdSimDivPickers.so to rdSimDivPickers.cpython-313-x86_64-linux-gnu.so +I: dh_python3 fs:421: renaming cDataStructs.so to cDataStructs.cpython-313-x86_64-linux-gnu.so +I: dh_python3 fs:421: renaming Clustering.so to Clustering.cpython-313-x86_64-linux-gnu.so +I: dh_python3 fs:421: renaming rdInfoTheory.so to rdInfoTheory.cpython-313-x86_64-linux-gnu.so +I: dh_python3 fs:421: renaming cQuantize.so to cQuantize.cpython-313-x86_64-linux-gnu.so dh_numpy3 -ppython3-rdkit Possible precedence issue with control flow operator (return) at /usr/bin/dh_numpy3 line 57. make[1]: Leaving directory '/build/reproducible-path/rdkit-202503.1' @@ -37677,22 +37714,22 @@ dh_strip -a -O--buildsystem=cmake dh_makeshlibs -a -O--buildsystem=cmake dh_shlibdeps -a -O--buildsystem=cmake -dpkg-shlibdeps: warning: debian/postgresql-17-rdkit/usr/lib/postgresql/17/lib/rdkit.so contains an unresolvable reference to symbol errmsg: it's probably a plugin -dpkg-shlibdeps: warning: 24 other similar warnings have been skipped (use -v to see them all) dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib64/ld-linux-x86-64.so.2 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib64/ld-linux-x86-64.so.2.usr-is-merged -dpkg-shlibdeps: warning: symbol PyExc_KeyError used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries +dpkg-shlibdeps: warning: debian/postgresql-17-rdkit/usr/lib/postgresql/17/lib/rdkit.so contains an unresolvable reference to symbol pg_detoast_datum: it's probably a plugin +dpkg-shlibdeps: warning: 24 other similar warnings have been skipped (use -v to see them all) dpkg-shlibdeps: warning: symbol PyExc_IndexError used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries -dpkg-shlibdeps: warning: symbol PyLong_FromUnsignedLong used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries +dpkg-shlibdeps: warning: symbol PyExc_KeyError used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyErr_SetString used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries -dpkg-shlibdeps: warning: symbol PyLong_FromLong used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries -dpkg-shlibdeps: warning: symbol PyErr_SetObject used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries +dpkg-shlibdeps: warning: symbol PyObject_IsTrue used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries +dpkg-shlibdeps: warning: symbol PyExc_ValueError used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyObject_CallFunction used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyExc_RuntimeError used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries -dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries -dpkg-shlibdeps: warning: symbol PyObject_IsTrue used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries +dpkg-shlibdeps: warning: symbol PyLong_FromLong used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries +dpkg-shlibdeps: warning: symbol PyErr_SetObject used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries +dpkg-shlibdeps: warning: symbol PyLong_FromUnsignedLong used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries dpkg-shlibdeps: warning: 2 other similar warnings have been skipped (use -v to see them all) dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib64/ld-linux-x86-64.so.2 @@ -37700,22 +37737,22 @@ diversion by libc6 to: /lib64/ld-linux-x86-64.so.2.usr-is-merged 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: Depends field of package rdkit-doc: 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: 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: Depends field of package rdkit-doc: 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: Depends field of package rdkit-data: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums -O--buildsystem=cmake dh_builddeb -O--buildsystem=cmake +dpkg-deb: building package 'librdkit1t64-dbgsym' in '../librdkit1t64-dbgsym_202503.1-4_amd64.deb'. dpkg-deb: building package 'python3-rdkit' in '../python3-rdkit_202503.1-4_amd64.deb'. dpkg-deb: building package 'python3-rdkit-dbgsym' in '../python3-rdkit-dbgsym_202503.1-4_amd64.deb'. dpkg-deb: building package 'rdkit-doc' in '../rdkit-doc_202503.1-4_all.deb'. +dpkg-deb: building package 'librdkit-dev' in '../librdkit-dev_202503.1-4_amd64.deb'. dpkg-deb: building package 'rdkit-data' in '../rdkit-data_202503.1-4_all.deb'. +dpkg-deb: building package 'postgresql-17-rdkit-dbgsym' in '../postgresql-17-rdkit-dbgsym_202503.1-4_amd64.deb'. dpkg-deb: building package 'librdkit1t64' in '../librdkit1t64_202503.1-4_amd64.deb'. -dpkg-deb: building package 'librdkit1t64-dbgsym' in '../librdkit1t64-dbgsym_202503.1-4_amd64.deb'. -dpkg-deb: building package 'librdkit-dev' in '../librdkit-dev_202503.1-4_amd64.deb'. dpkg-deb: building package 'postgresql-17-rdkit' in '../postgresql-17-rdkit_202503.1-4_amd64.deb'. -dpkg-deb: building package 'postgresql-17-rdkit-dbgsym' in '../postgresql-17-rdkit-dbgsym_202503.1-4_amd64.deb'. dpkg-genbuildinfo --build=binary -O../rdkit_202503.1-4_amd64.buildinfo dpkg-genchanges --build=binary -O../rdkit_202503.1-4_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -37723,12 +37760,14 @@ 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/1326071/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1326071/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/119717 and its subdirectories -I: Current time: Mon Aug 31 18:00:43 -12 2026 -I: pbuilder-time-stamp: 1788242443 +I: removing directory /srv/workspace/pbuilder/1326071 and its subdirectories +I: Current time: Wed Jul 30 14:54:44 +14 2025 +I: pbuilder-time-stamp: 1753836884