Diff of the two buildlogs: -- --- b1/build.log 2025-07-18 06:06:39.784348324 +0000 +++ b2/build.log 2025-07-18 06:30:05.554098946 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Aug 20 00:10:13 -12 2026 -I: pbuilder-time-stamp: 1787227813 +I: Current time: Fri Jul 18 20:06:44 +14 2025 +I: pbuilder-time-stamp: 1752818804 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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/2042499/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1069129/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 18 06:07 /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/1069129/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1069129/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='unstable' - 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=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='df5c58bc7ef345fe87d9fb180e5f4d7b' - 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='2042499' - PS1='# ' - PS2='> ' + INVOCATION_ID=d03906c62aa64eb6b8a1de105613b890 + 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=1069129 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.lvWsFG6n/pbuilderrc_9HXf --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.lvWsFG6n/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.lvWsFG6n/pbuilderrc_xb1I --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.lvWsFG6n/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 6.12.32+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.32-1~bpo12+1 (2025-06-21) 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/2042499/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 12 19:25 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1069129/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 unstable/main amd64 texlive-latex-recommended all 2024.20250309-1 [8745 kB] Get: 368 http://deb.debian.org/debian unstable/main amd64 texlive-pictures all 2024.20250309-1 [17.0 MB] Get: 369 http://deb.debian.org/debian unstable/main amd64 texlive-latex-extra all 2024.20250309-2 [25.2 MB] -Fetched 421 MB in 9s (49.0 MB/s) +Fetched 421 MB in 49s (8551 kB/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 ... 19849 files and directories currently installed.) @@ -1758,8 +1790,8 @@ Setting up tzdata (2025b-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Thu Aug 20 12:12:55 UTC 2026. -Universal Time is now: Thu Aug 20 12:12:55 UTC 2026. +Local time is now: Fri Jul 18 06:11:35 UTC 2025. +Universal Time is now: Fri Jul 18 06:11:35 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/1069129/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/1069129/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 (1.2s) +-- Configuring done (4.9s) +-- Generating done (2.2s) CMake Warning: Manually-specified variables were not used by the project: @@ -2330,14 +2366,14 @@ command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. --- Configuring done (0.7s) +-- Configuring done (0.5s) -- Generating done (0.0s) -- Build files have been written to: /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/build-17 make[1]: Leaving directory '/build/reproducible-path/rdkit-202503.1' debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/rdkit-202503.1' dh_auto_build - cd obj-x86_64-linux-gnu && make -j42 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-x86_64-linux-gnu && make -j40 "INSTALL=install --strip-program=true" VERBOSE=1 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 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//CMakeFiles/progress.marks @@ -2370,69 +2406,69 @@ 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[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/build.make External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f External/INCHI-API/CMakeFiles/inchi_support.dir/build.make External/INCHI-API/CMakeFiles/inchi_support.dir/build -make -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make Code/RDGeneral/CMakeFiles/RDGeneral.dir/build make[4]: Leaving directory 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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 External/GA/CMakeFiles/ga.dir/ga/StringChromosome.cpp.o -MF CMakeFiles/ga.dir/ga/StringChromosome.cpp.o.d -o CMakeFiles/ga.dir/ga/StringChromosome.cpp.o -c /build/reproducible-path/rdkit-202503.1/External/GA/ga/StringChromosome.cpp +[ 1%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/RDLog.cpp.o +[ 1%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/Invariant.cpp.o [ 1%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/types.cpp.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 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Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/LocaleSwitcher.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 -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 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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/RDGeneral/CMakeFiles/rdkitCatch.dir/catch_main.cpp.o -MF CMakeFiles/rdkitCatch.dir/catch_main.cpp.o.d -o CMakeFiles/rdkitCatch.dir/catch_main.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/catch_main.cpp +[ 2%] Building CXX object External/GA/CMakeFiles/ga.dir/util/RandomUtil.cpp.o +[ 2%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/versions.cpp.o +[ 2%] Building C object Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hc.c.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/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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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/RDStreams/CMakeFiles/RDStreams.dir/streams.cpp.o -MF CMakeFiles/RDStreams.dir/streams.cpp.o.d -o CMakeFiles/RDStreams.dir/streams.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/RDStreams/streams.cpp -[ 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/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 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-DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/RDStreams/CMakeFiles/RDStreams.dir/streams.cpp.o -MF CMakeFiles/RDStreams.dir/streams.cpp.o.d -o CMakeFiles/RDStreams.dir/streams.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/RDStreams/streams.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 @@ -2440,14 +2476,14 @@ cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_symlink_library ../../../../lib/libRDKithc.so.1.2025.03.1 ../../../../lib/libRDKithc.so.1 ../../../../lib/libRDKithc.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 2%] Built target hc -[ 2%] Linking CXX static library librdkitCatch.a -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -P CMakeFiles/rdkitCatch.dir/cmake_clean_target.cmake [ 2%] Linking CXX shared library ../../lib/libRDKitga.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/External/GA && /usr/bin/cmake -E cmake_link_script CMakeFiles/ga.dir/link.txt --verbose=1 -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdkitCatch.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/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 CMakeFiles/ga.dir/util/Util.cpp.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 cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/External/GA && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitga.so.1.2025.03.1 ../../lib/libRDKitga.so.1 ../../lib/libRDKitga.so +[ 2%] Linking CXX static library librdkitCatch.a +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -P CMakeFiles/rdkitCatch.dir/cmake_clean_target.cmake 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/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdkitCatch.dir/link.txt --verbose=1 [ 2%] Built target ga /usr/bin/ar qc librdkitCatch.a CMakeFiles/rdkitCatch.dir/catch_main.cpp.o /usr/bin/ranlib librdkitCatch.a @@ -2470,30 +2506,30 @@ make -f Code/RDBoost/CMakeFiles/RDBoost.dir/build.make Code/RDBoost/CMakeFiles/RDBoost.dir/depend make -f Code/RDGeneral/CMakeFiles/testDict.dir/build.make Code/RDGeneral/CMakeFiles/testDict.dir/depend make -f Code/RDGeneral/CMakeFiles/testRDValue.dir/build.make Code/RDGeneral/CMakeFiles/testRDValue.dir/depend +make -f Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build.make Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-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/DataStructs /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/DataStructs.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/Numerics/EigenSolvers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics/EigenSolvers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/DependInfo.cmake "--color=" -make -f Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build.make Code/RDGeneral/CMakeFiles/testConcurrentQueue.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/RDBoost /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDBoost /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDBoost/CMakeFiles/RDBoost.dir/DependInfo.cmake "--color=" make -f Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/build.make Code/RDGeneral/CMakeFiles/dictTestsCatch.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/RDGeneral /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/testDict.dir/DependInfo.cmake "--color=" +make -f Code/RDGeneral/CMakeFiles/logTestsCatch.dir/build.make Code/RDGeneral/CMakeFiles/logTestsCatch.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/RDGeneral /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/testRDValue.dir/DependInfo.cmake "--color=" -make -f Code/RDGeneral/CMakeFiles/logTestsCatch.dir/build.make Code/RDGeneral/CMakeFiles/logTestsCatch.dir/depend make -f Code/Numerics/CMakeFiles/testMatrices.dir/build.make Code/Numerics/CMakeFiles/testMatrices.dir/depend +make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make Code/Catalogs/CMakeFiles/Catalogs.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/RDGeneral /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/DependInfo.cmake "--color=" -make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make Code/Catalogs/CMakeFiles/Catalogs.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/RDGeneral /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/dictTestsCatch.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/RDGeneral /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/logTestsCatch.dir/DependInfo.cmake "--color=" -make -f Code/Query/CMakeFiles/testQuery.dir/build.make Code/Query/CMakeFiles/testQuery.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 /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics/CMakeFiles/testMatrices.dir/DependInfo.cmake "--color=" +make -f Code/Query/CMakeFiles/testQuery.dir/build.make Code/Query/CMakeFiles/testQuery.dir/depend make -f Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build.make Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-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/Catalogs /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Catalogs /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Catalogs/CMakeFiles/Catalogs.dir/DependInfo.cmake "--color=" @@ -2507,144 +2543,146 @@ 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[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build.make Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make Code/DataStructs/CMakeFiles/DataStructs.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/RDGeneral/CMakeFiles/testDict.dir/build.make Code/RDGeneral/CMakeFiles/testDict.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[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build.make Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.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/RDBoost/CMakeFiles/RDBoost.dir/build.make Code/RDBoost/CMakeFiles/RDBoost.dir/build -make -f Code/RDGeneral/CMakeFiles/testDict.dir/build.make Code/RDGeneral/CMakeFiles/testDict.dir/build make -f 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build.make Code/RDGeneral/CMakeFiles/testConcurrentQueue.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' -[ 2%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/BitVect.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/BitVect.cpp.o -MF CMakeFiles/DataStructs.dir/BitVect.cpp.o.d -o CMakeFiles/DataStructs.dir/BitVect.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DataStructs/BitVect.cpp -[ 4%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogParams.cpp.o +[ 3%] Building CXX object Code/RDGeneral/CMakeFiles/testDict.dir/testDict.cpp.o +[ 3%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/Utils.cpp.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/RDGeneral/CMakeFiles/testDict.dir/testDict.cpp.o -MF CMakeFiles/testDict.dir/testDict.cpp.o.d -o CMakeFiles/testDict.dir/testDict.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/testDict.cpp +[ 4%] Building CXX object Code/Query/CMakeFiles/testQuery.dir/test.cpp.o +[ 4%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o +[ 4%] Building CXX object Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/testConcurrentQueue.cpp.o +cd 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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/RDGeneral/CMakeFiles/testConcurrentQueue.dir/testConcurrentQueue.cpp.o -MF CMakeFiles/testConcurrentQueue.dir/testConcurrentQueue.cpp.o.d -o CMakeFiles/testConcurrentQueue.dir/testConcurrentQueue.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/testConcurrentQueue.cpp +[ 5%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/SparseBitVect.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 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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/RDBoost/CMakeFiles/RDBoost.dir/Wrap.cpp.o -MF CMakeFiles/RDBoost.dir/Wrap.cpp.o.d -o CMakeFiles/RDBoost.dir/Wrap.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/RDBoost/Wrap.cpp +[ 5%] Building CXX object Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o 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 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-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/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 -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 -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/RealValueVect.cpp.o -MF CMakeFiles/DataStructs.dir/RealValueVect.cpp.o.d -o CMakeFiles/DataStructs.dir/RealValueVect.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DataStructs/RealValueVect.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 -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/DistPicker.cpp.o -MF CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o.d -o CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/SimDivPickers/DistPicker.cpp +[ 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%] Linking CXX executable testMatCalc +[ 7%] Built target testConcurrentQueue 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 +[ 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++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 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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++ -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 && /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/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' 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' -[ 7%] Built target testConcurrentQueue [ 7%] Building CXX object Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/testPickers.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 -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 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-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 Catalogs -[ 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 /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' -[ 7%] Built target logTestsCatch [ 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 +[ 7%] Built target logTestsCatch +[ 7%] Built target Catalogs /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 testMatrices [ 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' @@ -2656,14 +2694,10 @@ make -f Code/DataStructs/CMakeFiles/catchDataStructs.dir/build.make Code/DataStructs/CMakeFiles/catchDataStructs.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/Geometry /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/RDGeometryLib.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/DataStructs /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/testDataStructs.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/DataStructs /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/testFPB.dir/DependInfo.cmake "--color=" make -f Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build.make Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/depend +make -f Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build.make Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-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/DataStructs /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/testMultiFPB.dir/DependInfo.cmake "--color=" -make -f Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build.make Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-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/DataStructs /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/catchDataStructs.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' @@ -2672,64 +2706,66 @@ 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/ML/InfoTheory /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ML/InfoTheory /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ML/InfoTheory/CMakeFiles/InfoTheory.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[4]: Leaving 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 -make -f Code/DataStructs/CMakeFiles/testFPB.dir/build.make Code/DataStructs/CMakeFiles/testFPB.dir/build +make -f Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build.make Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build.make Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/DataStructs/CMakeFiles/testDataStructs.dir/build.make Code/DataStructs/CMakeFiles/testDataStructs.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build.make Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build make -f Code/DataStructs/CMakeFiles/testMultiFPB.dir/build.make Code/DataStructs/CMakeFiles/testMultiFPB.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/DataStructs/CMakeFiles/catchDataStructs.dir/build.make Code/DataStructs/CMakeFiles/catchDataStructs.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/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build.make Code/ML/InfoTheory/CMakeFiles/InfoTheory.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]: 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 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/DataStructs /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/testDataStructs.dir/DependInfo.cmake "--color=" +[ 9%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/UniformRealValueGrid3D.cpp.o make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 10%] Building CXX object Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o -[ 10%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o -[ 10%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/point.cpp.o -[ 10%] Building CXX object Code/DataStructs/CMakeFiles/testFPB.dir/testFPB.cpp.o -[ 10%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o -[ 10%] Building CXX object Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/catch_tests.cpp.o +[ 9%] Building CXX object Code/DataStructs/CMakeFiles/catchDataStructs.dir/catch_tests.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 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Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o -[ 10%] Building CXX object Code/DataStructs/CMakeFiles/catchDataStructs.dir/catch_tests.cpp.o -[ 10%] Building CXX object Code/DataStructs/CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o -[ 10%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o -[ 10%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/UniformRealValueGrid3D.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 -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o -MF CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o.d -o CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ML/InfoTheory/InfoBitRanker.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 -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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/DataStructs/CMakeFiles/testFPB.dir/testFPB.cpp.o -MF CMakeFiles/testFPB.dir/testFPB.cpp.o.d -o CMakeFiles/testFPB.dir/testFPB.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DataStructs/testFPB.cpp +[ 10%] Building CXX object Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/catch_tests.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 -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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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CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DataStructs/testDatastructs.cpp +[ 10%] Building CXX object Code/DataStructs/CMakeFiles/testFPB.dir/testFPB.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 -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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/DataStructs/CMakeFiles/testFPB.dir/testFPB.cpp.o -MF CMakeFiles/testFPB.dir/testFPB.cpp.o.d -o CMakeFiles/testFPB.dir/testFPB.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DataStructs/testFPB.cpp [ 10%] Linking CXX executable testQuery cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Query && /usr/bin/cmake -E cmake_link_script CMakeFiles/testQuery.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/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' [ 10%] Built target testQuery +[ 10%] Linking CXX executable testSimDivPickers +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSimDivPickers.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/testSimDivPickers.dir/link.d CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o -o testSimDivPickers ../../lib/libRDKitSimDivPickers.so.1.2025.03.1 ../../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 +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 10%] Built target testSimDivPickers [ 10%] Linking CXX shared library ../../lib/libRDKitRDBoost.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDBoost && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDBoost.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/RDBoost.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDBoost.so.1 -o ../../lib/libRDKitRDBoost.so.1.2025.03.1 CMakeFiles/RDBoost.dir/Wrap.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 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 @@ -2738,12 +2774,12 @@ [ 10%] Built target RDBoost make -f Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build.make Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/depend make -f Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build.make Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build.make Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-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/RDBoost/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDBoost/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/DependInfo.cmake "--color=" +make -f Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build.make Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-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/DataStructs/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DependInfo.cmake "--color=" -make -f Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build.make Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/depend make -f Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.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/DataManip/MetricMatrixCalc/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/DependInfo.cmake "--color=" @@ -2752,94 +2788,68 @@ 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/ML/Cluster/Murtagh /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build.make Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.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/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build.make Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build make -f Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build.make Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build +make -f Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build.make 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Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 10%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o +[ 11%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DataStructs.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 -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 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Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o -[ 11%] Building CXX object Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/RDBase.cpp.o -[ 12%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DataStructs.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/SimDivPickers/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 -DrdSimDivPickers_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/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o -MF CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o.d -o CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/SimDivPickers/Wrap/MaxMinPicker.cpp -[ 12%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o -[ 12%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDBoost/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 -DrdBase_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/RDBoost/Wrap/CMakeFiles/rdBase.dir/RDBase.cpp.o -MF CMakeFiles/rdBase.dir/RDBase.cpp.o.d -o CMakeFiles/rdBase.dir/RDBase.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/RDBoost/Wrap/RDBase.cpp +[ 11%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o +[ 11%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o +[ 11%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o +[ 11%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.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 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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/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o -MF CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o.d -o CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ML/InfoTheory/Wrap/rdInfoTheory.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/RDGeometryLib.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDGeometryLib.so.1 -o ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 CMakeFiles/RDGeometryLib.dir/point.cpp.o CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o CMakeFiles/RDGeometryLib.dir/UniformRealValueGrid3D.cpp.o CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o ../../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/Geometry && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1 ../../lib/libRDKitRDGeometryLib.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 13%] Built target RDGeometryLib +[ 12%] Built target RDGeometryLib make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make Code/GraphMol/CMakeFiles/GraphMol.dir/depend make -f Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/Alignment.dir/depend make -f Code/Geometry/CMakeFiles/testTransforms.dir/build.make Code/Geometry/CMakeFiles/testTransforms.dir/depend @@ -2849,19 +2859,17 @@ make -f Code/Geometry/CMakeFiles/geometryTestsCatch.dir/build.make Code/Geometry/CMakeFiles/geometryTestsCatch.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/Numerics/Alignment /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics/Alignment /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics/Alignment/CMakeFiles/Alignment.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/GraphMol.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/Geometry /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/testTransforms.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/GraphMol.dir/DependInfo.cmake "--color=" make -f Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build.make Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-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/Geometry /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/testGrid.dir/DependInfo.cmake "--color=" +make -f Code/Numerics/CMakeFiles/testConrec.dir/build.make Code/Numerics/CMakeFiles/testConrec.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/Geometry /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/testRealValueGrid.dir/DependInfo.cmake "--color=" -make -f Code/Numerics/CMakeFiles/testConrec.dir/build.make Code/Numerics/CMakeFiles/testConrec.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/Geometry /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/geometryTestsCatch.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/Geometry /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/testGrid.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/Geometry/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry/Wrap/CMakeFiles/rdGeometry.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/Geometry /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/geometryTestsCatch.dir/DependInfo.cmake "--color=" make -f Code/Features/CMakeFiles/testBaseFeatures.dir/build.make Code/Features/CMakeFiles/testBaseFeatures.dir/depend make -f Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' @@ -2870,265 +2878,293 @@ 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/Features /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Features 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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[4]: Leaving 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' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/Alignment.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]: Leaving directory '/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 -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/Wrap/CMakeFiles/rdGeometry.dir/build.make Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/Numerics/CMakeFiles/testConrec.dir/build.make Code/Numerics/CMakeFiles/testConrec.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[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]: 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]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/Numerics/CMakeFiles/testConrec.dir/build.make Code/Numerics/CMakeFiles/testConrec.dir/build +make -f Code/Features/CMakeFiles/testBaseFeatures.dir/build.make Code/Features/CMakeFiles/testBaseFeatures.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/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.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/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build.make Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 13%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Atom.cpp.o +[ 13%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryAtom.cpp.o [ 13%] Building CXX object 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Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/Point.cpp.o -[ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/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 -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 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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 -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/QueryAtom.cpp.o -MF CMakeFiles/GraphMol.dir/QueryAtom.cpp.o.d -o CMakeFiles/GraphMol.dir/QueryAtom.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/QueryAtom.cpp -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 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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/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 +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 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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/Numerics/Alignment/CMakeFiles/Alignment.dir/AlignPoints.cpp.o -MF CMakeFiles/Alignment.dir/AlignPoints.cpp.o.d -o CMakeFiles/Alignment.dir/AlignPoints.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Numerics/Alignment/AlignPoints.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 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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 -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdInfoTheory_EXPORTS -I/build/reproducible-path/rdkit-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/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o -MF CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o.d -o CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ML/InfoTheory/Wrap/BitCorrMatGenerator.cpp [ 15%] Linking CXX shared module ../../../../rdkit/ML/Cluster/Clustering.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/Clustering.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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object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryOps.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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-DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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/atomic_data.cpp.o -MF CMakeFiles/GraphMol.dir/atomic_data.cpp.o.d -o CMakeFiles/GraphMol.dir/atomic_data.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/atomic_data.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/testFPB.dir/link.d CMakeFiles/testFPB.dir/testFPB.cpp.o -o testFPB ../../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' -[ 16%] Built target ChemicalFeatures -[ 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++ 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CMakeFiles/GraphMol.dir/Canon.cpp.o.d -o CMakeFiles/GraphMol.dir/Canon.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Canon.cpp +[ 15%] Built target testFPB +[ 15%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/rdInfoTheory.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 -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdInfoTheory_EXPORTS -I/build/reproducible-path/rdkit-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/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o -MF CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o.d -o CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ML/InfoTheory/Wrap/rdInfoTheory.cpp +[ 15%] Linking CXX shared library ../../../lib/libRDKitAlignment.so +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/Alignment.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/Alignment.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitAlignment.so.1 -o ../../../lib/libRDKitAlignment.so.1.2025.03.1 CMakeFiles/Alignment.dir/AlignPoints.cpp.o ../../../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/Numerics/Alignment && /usr/bin/cmake -E cmake_symlink_library 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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/ChemicalFeatures /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ChemicalFeatures /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/DependInfo.cmake "--color=" -/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 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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/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o -MF CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o.d -o CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ChemicalFeatures/testChemicalFeatures.cpp -[ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AddHs.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 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/testTransforms.dir/link.txt --verbose=1 -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 18%] Building CXX object Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/testAlignment.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics/Alignment && /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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19%] Linking CXX executable testRealValueGrid +[ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolPickler.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 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Code/GraphMol/CMakeFiles/GraphMol.dir/FindStereo.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 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Atropisomers.cpp [ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/WedgeBonds.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/WedgeBonds.cpp.o -MF CMakeFiles/GraphMol.dir/WedgeBonds.cpp.o.d -o CMakeFiles/GraphMol.dir/WedgeBonds.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/WedgeBonds.cpp -[ 20%] Linking CXX shared module ../../../rdkit/SimDivFilters/rdSimDivPickers.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSimDivPickers.dir/link.txt --verbose=1 [ 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 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../../../lib/libRDKithc.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' -[ 20%] Built target rdSimDivPickers -[ 20%] Linking CXX executable testChemicalFeatures -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/testChemicalFeatures.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated 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-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/rdInfoTheory.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/ML/InfoTheory/rdInfoTheory.so CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o ../../../../lib/libRDKitInfoTheory.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.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' [ 20%] Built target rdInfoTheory -[ 20%] Linking CXX executable testDataStructs -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDataStructs.dir/link.txt --verbose=1 -[ 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=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/testDataStructs.dir/link.d CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o -o testDataStructs ../../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' -[ 20%] Built target testDataStructs -/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/testAlignment.dir/link.d CMakeFiles/testAlignment.dir/testAlignment.cpp.o -o testAlignment ../../../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' -[ 20%] Built target testAlignment [ 20%] Linking CXX shared module ../../../../rdkit/Numerics/rdAlignment.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics/Alignment/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdAlignment.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong 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Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 20%] Built target rdAlignment +[ 20%] Linking CXX executable testDataStructs +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDataStructs.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/testDataStructs.dir/link.d CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o -o testDataStructs ../../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' +[ 20%] Built target testDataStructs [ 20%] Linking CXX shared module ../../../rdkit/Geometry/rdGeometry.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdGeometry.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/rdGeometry.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Geometry/rdGeometry.so CMakeFiles/rdGeometry.dir/Point.cpp.o CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o CMakeFiles/rdGeometry.dir/UniformRealValueGrid3D.cpp.o CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitRDBoost.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 @@ -3153,158 +3189,154 @@ 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/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/Trajectory /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/depend make -f Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/depend +make -f Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/depend +make -f Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build.make 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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 /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/tableTestsCatch.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/Trajectory /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu 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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/ChemicalFeatures/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.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/GenericGroups /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups 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/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/PartialCharges.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/build.make Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.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/MolCatalog 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Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o -MF CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o.d -o CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse/SmilesWrite.cpp 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/configs/Tetrahedral.cpp.o -MF CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o.d -o CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/configs/Tetrahedral.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 -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/CXSmilesOps.cpp.o -MF CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o.d -o CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse/CXSmilesOps.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 -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/SmilesJSONParsers.cpp.o -MF CMakeFiles/SmilesParse.dir/SmilesJSONParsers.cpp.o.d -o CMakeFiles/SmilesParse.dir/SmilesJSONParsers.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse/SmilesJSONParsers.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 -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/smarts.tab.cpp.o -MF CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o.d -o CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse/smarts.tab.cpp [ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/AtropisomerBond.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/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/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o @@ -3313,8 +3345,12 @@ 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 [ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule2.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/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/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs && /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_SUBGRAPHS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubgraphs_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -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/Subgraphs/CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o -MF CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o.d -o CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Subgraphs/SubgraphUtils.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/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o +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 -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 [ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4a.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/Rule4a.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/rules/Rule4a.cpp [ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o @@ -3325,44 +3361,44 @@ 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/Rule5.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/rules/Rule5.cpp [ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5New.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/Rule5New.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/rules/Rule5New.cpp -[ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule6.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/Rule6.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/rules/Rule6.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%] Building CXX object 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%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule6.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/Rule6.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/rules/Rule6.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' [ 24%] Built target tableTestsCatch +[ 24%] Building CXX object 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 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 +[ 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/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 +/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 +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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 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 /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]: 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' -[ 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%] Building CXX object Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/rdMolCatalog.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 -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 -DrdMolCatalog_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/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o -MF CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o.d -o CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolCatalog/Wrap/rdMolCatalog.cpp -[ 24%] Linking CXX shared library ../../../lib/libRDKitTrajectory.so -cd 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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/PartialCharges && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitPartialCharges.so.1.2025.03.1 ../../../lib/libRDKitPartialCharges.so.1 ../../../lib/libRDKitPartialCharges.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 24%] Built target PartialCharges +[ 24%] Building CXX object Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o make -f Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build.make Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/depend +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 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'/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[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 24%] Building CXX object Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o +[ 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 cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/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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-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 /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/Trajectory && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/libRDKitTrajectory.so.1 ../../../lib/libRDKitTrajectory.so @@ -3375,25 +3411,19 @@ 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 /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/DependInfo.cmake "--color=" make[4]: Leaving 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-Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/LinearSearch.cpp.o -MF CMakeFiles/Optimizer.dir/LinearSearch.cpp.o.d -o CMakeFiles/Optimizer.dir/LinearSearch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Numerics/Optimizer/LinearSearch.cpp +[ 24%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o [ 24%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/rdTrajectory.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 -Drdtrajectory_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/Wrap/CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o -MF CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o.d -o CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/Trajectory.cpp 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/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 -[ 24%] Linking CXX shared library ../../../lib/libRDKitSubgraphs.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/Subgraphs.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/Subgraphs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSubgraphs.so.1 -o ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o CMakeFiles/Subgraphs.dir/SubgraphUtils.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/Subgraphs && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1 ../../../lib/libRDKitSubgraphs.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 24%] Built target Subgraphs [ 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=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/Optimizer.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitOptimizer.so.1 -o ../../../lib/libRDKitOptimizer.so.1.2025.03.1 CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o CMakeFiles/Optimizer.dir/LinearSearch.cpp.o ../../../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 @@ -3407,92 +3437,82 @@ 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/ForceField.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/ForceField/CMakeFiles/ForceField.dir/build.make Code/ForceField/CMakeFiles/ForceField.dir/build +make -f Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 24%] 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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build +make -f Code/ForceField/CMakeFiles/ForceField.dir/build.make Code/ForceField/CMakeFiles/ForceField.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 24%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/ForceField.cpp.o +[ 24%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics/Optimizer && /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/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/DistanceConstraint.cpp.o +[ 24%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/ForceField.cpp.o [ 24%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/AngleConstraints.cpp.o [ 24%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/DistanceConstraints.cpp.o -[ 24%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/DistanceConstraint.cpp.o 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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 -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/AngleConstraint.cpp.o -MF CMakeFiles/ForceField.dir/AngleConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/AngleConstraint.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/AngleConstraint.cpp -[ 24%] 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 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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/UFF/AngleBend.cpp.o +[ 25%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o +[ 25%] Building 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 -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/AngleConstraints.cpp.o -MF CMakeFiles/ForceField.dir/AngleConstraints.cpp.o.d -o CMakeFiles/ForceField.dir/AngleConstraints.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/AngleConstraints.cpp +[ 25%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o +[ 25%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Utils.cpp.o +[ 25%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Inversions.cpp.o +[ 25%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Params.cpp.o +[ 25%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/TorsionAngle.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 -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 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/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 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/DistanceConstraints.cpp.o -MF CMakeFiles/ForceField.dir/DistanceConstraints.cpp.o.d -o CMakeFiles/ForceField.dir/DistanceConstraints.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/DistanceConstraints.cpp -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics/Optimizer && /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/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/PositionConstraint.cpp.o -MF CMakeFiles/ForceField.dir/PositionConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/PositionConstraint.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/PositionConstraint.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 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CMakeFiles/GenericGroups.dir/GenericGroups.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/GenericGroups && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1 ../../../lib/libRDKitGenericGroups.so +[ 26%] Linking CXX shared module ../../../rdkit/Chem/rdChemicalFeatures.so +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 +/usr/bin/c++ -fPIC -g -O2 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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/MMFF/AngleBend.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/AngleBend.cpp +[ 27%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/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 -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -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/ForceField/CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/StretchBend.cpp +[ 27%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/OopBend.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 -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/OopBend.cpp +/usr/bin/c++ 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/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1 ../../../lib/libRDKitSubgraphs.so +[ 27%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionAngle.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 -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/TorsionAngle.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 27%] Building 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-Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/Nonbonded.cpp +[ 27%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Params.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 -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Params.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/Params.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/Params.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/Params.cpp [ 27%] Linking CXX shared library ../../../lib/libRDKitMolTransforms.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolTransforms.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/MolTransforms.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolTransforms.so.1 -o ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.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 @@ -3506,27 +3526,43 @@ 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 /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.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/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build.make Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build +make -f Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 27%] Building CXX object Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/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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CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolTransforms/Wrap/rdMolTransforms.cpp [ 27%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/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 -DrdMolTransforms_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/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o -MF CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o.d -o CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolTransforms/Wrap/rdMolTransforms.cpp [ 27%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers && /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_SHAPEHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -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/ShapeEncoder.cpp.o -MF CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o.d -o CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ShapeHelpers/ShapeEncoder.cpp cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers && /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_SHAPEHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -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 -[ 28%] 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 -/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/rdPartialCharges.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdPartialCharges.so CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o ../../../../lib/libRDKitPartialCharges.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 +[ 27%] Linking CXX shared library ../../../lib/libRDKitGenericGroups.so +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups && /usr/bin/cmake -E cmake_link_script CMakeFiles/GenericGroups.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 ../../../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/GenericGroups && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1 ../../../lib/libRDKitGenericGroups.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 28%] Built target rdPartialCharges -[ 28%] Linking CXX executable testOptimizer +[ 27%] Built target GenericGroups +make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-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/SubstructMatch.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 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 /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 -DRDKIT_SUBSTRUCTMATCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructMatch_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/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 +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 -DRDKIT_SUBSTRUCTMATCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructMatch_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/Substruct/CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -MF CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o.d -o CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Substruct/SubstructUtils.cpp +[ 27%] Linking CXX executable testOptimizer 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 +[ 28%] 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 /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/testOptimizer.dir/link.d CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -o testOptimizer ../../../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' +/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/rdPartialCharges.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdPartialCharges.so CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o ../../../../lib/libRDKitPartialCharges.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' [ 28%] Built target testOptimizer +[ 28%] Built target rdPartialCharges [ 28%] Linking CXX shared library ../../../lib/libRDKitSLNParse.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/SLNParse.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/SLNParse.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSLNParse.so.1 -o ../../../lib/libRDKitSLNParse.so.1.2025.03.1 CMakeFiles/SLNParse.dir/SLNParse.cpp.o CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o CMakeFiles/SLNParse.dir/sln.tab.cpp.o CMakeFiles/SLNParse.dir/lex.yysln.cpp.o ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../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 @@ -3541,27 +3577,21 @@ 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 /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/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 -DrdSLNParse_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/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 -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdtrajectory.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdtrajectory.so CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../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 ../../../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' -[ 29%] Built target rdtrajectory -[ 29%] Linking CXX shared module ../../../../rdkit/Chem/rdCIPLabeler.so +[ 28%] 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 /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/rdCIPLabeler.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdCIPLabeler.so CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o ../../../../lib/libRDKitCIPLabeler.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' -[ 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 -[ 29%] Built target rdCIPLabeler -/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 +[ 28%] Built target rdCIPLabeler +[ 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 [ 29%] 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 -Wl,--dependency-file=CMakeFiles/ShapeHelpers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitShapeHelpers.so.1 -o ../../../lib/libRDKitShapeHelpers.so.1.2025.03.1 CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o ../../../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 cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitShapeHelpers.so.1.2025.03.1 ../../../lib/libRDKitShapeHelpers.so.1 ../../../lib/libRDKitShapeHelpers.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 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdtrajectory.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdtrajectory.so CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../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 ../../../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' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 29%] Built target rdtrajectory [ 29%] 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' @@ -3571,16 +3601,22 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 29%] Building CXX object Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/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 -DrdShapeHelpers_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/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o -MF CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o.d -o CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ShapeHelpers/Wrap/rdShapeHelpers.cpp +[ 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 [ 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 -Werror=format-security -fcf-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/rdqueries.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdqueries.so CMakeFiles/rdqueries.dir/rdqueries.cpp.o CMakeFiles/rdqueries.dir/Queries.cpp.o ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../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 rdqueries [ 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 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdqueries.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdqueries.so CMakeFiles/rdqueries.dir/rdqueries.cpp.o CMakeFiles/rdqueries.dir/Queries.cpp.o ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../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' +/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 +[ 30%] Built target rdqueries [ 30%] Built target rdMolCatalog +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 30%] Built target ForceField [ 30%] 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 /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 @@ -3595,6 +3631,16 @@ 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 +[ 30%] Linking CXX shared module ../../../../rdkit/Chem/rdMolTransforms.so +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolTransforms.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 +/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/rdMolTransforms.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolTransforms.so CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o ../../../../lib/libRDKitMolTransforms.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/libRDKitEigenSolvers.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 rdMolTransforms [ 31%] 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 @@ -3608,102 +3654,87 @@ make -f Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/molbundleTestsCatch.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/SmilesParse/CMakeFiles/smiTest2.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.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/graphmolIterTest.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/depend +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/graphmolMemTest1.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/queryTestsCatch.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-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/SmilesParse/CMakeFiles/v2smiTestCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/v2smiTestCatch.dir/depend -make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-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/smiTest2.dir/DependInfo.cmake "--color=" -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/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[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 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/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]: 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/queryTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/queryTestsCatch.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[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/graphmolcpTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/depend make -f Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build make -f Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build +make -f Code/GraphMol/CMakeFiles/queryTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/queryTestsCatch.dir/build make -f Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/build -make[4]: Entering 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/SmilesParse/CMakeFiles/v2smiTestCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/v2smiTestCatch.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]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 31%] Building CXX object Code/GraphMol/CMakeFiles/queryTestsCatch.dir/catch_queries.cpp.o -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' -[ 31%] Building CXX object Code/GraphMol/CMakeFiles/graphmolIterTest.dir/itertest.cpp.o -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f 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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 -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/PartialCharges/CMakeFiles/testPartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build -cd 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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 -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 CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/memtest1.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/depend make[4]: Entering directory 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-fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolcpTest.dir/cptest.cpp.o -MF CMakeFiles/graphmolcpTest.dir/cptest.cpp.o.d -o CMakeFiles/graphmolcpTest.dir/cptest.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/cptest.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 -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 CMakeFiles/smiTest2.dir/test2.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse/test2.cpp 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]: 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=" +[ 31%] Building CXX object Code/GraphMol/CMakeFiles/graphmolIterTest.dir/itertest.cpp.o +[ 31%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/test2.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 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/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' -[ 32%] Built target rdSLNParse -[ 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 && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolTransforms.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/rdMolTransforms.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolTransforms.so CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o ../../../../lib/libRDKitMolTransforms.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/libRDKitEigenSolvers.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' -[ 32%] Built target rdMolTransforms -[ 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 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -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 +[ 32%] Building CXX object Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/test1.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges && /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/PartialCharges/CMakeFiles/testPartialCharges.dir/test1.cpp.o -MF CMakeFiles/testPartialCharges.dir/test1.cpp.o.d -o CMakeFiles/testPartialCharges.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/PartialCharges/test1.cpp [ 32%] 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 /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 @@ -3713,229 +3744,234 @@ make -f Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/depend make -f Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/depend make -f Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/depend -make -f Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/moliteratorTestsCatch.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/MolAlign.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/depend make -f Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.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/ForceFieldHelpers /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 /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.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/graphmolqueryTest.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-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[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 /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 /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.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/ForceFieldHelpers /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 /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/DependInfo.cmake "--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/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.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/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/smaTest1.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-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/Fingerprints /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-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/FragCatalog /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.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/moliteratorTestsCatch.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/FilterCatalog /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 /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.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/Fingerprints /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints 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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 -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/smatest.cpp.o -MF CMakeFiles/smaTest1.dir/smatest.cpp.o.d -o CMakeFiles/smaTest1.dir/smatest.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse/smatest.cpp -[ 32%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o -[ 33%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o -[ 33%] Building CXX object 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 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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/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o -MF CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FragCatalog/FragCatalogEntry.cpp cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /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 -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/CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o -MF CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o.d -o CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/PatternFingerprints.cpp +[ 35%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/test.cpp.o +[ 35%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o +cd 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Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o -MF CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.cpp +[ 37%] Linking CXX executable smiTest2 +[ 37%] Linking CXX executable testPartialCharges +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_link_script CMakeFiles/testPartialCharges.dir/link.txt --verbose=1 +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 +[ 37%] 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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-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/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o -MF CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FragCatalog/FragCatParams.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 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object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.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 -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-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/MolChemicalFeatureFactory.cpp.o -MF CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o.d -o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.cpp +[ 37%] Built target testPartialCharges +[ 37%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog && /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 -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK 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CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FragCatalog/FragFPGenerator.cpp +[ 37%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/FeatureParser.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 -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g 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CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/AtomPairs.cpp +[ 37%] Linking CXX executable subgraphsCatch +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/subgraphsCatch.dir/link.txt --verbose=1 +[ 38%] Linking CXX executable graphmolMemTest1 +[ 38%] 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 +/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/subgraphsCatch.dir/link.d CMakeFiles/subgraphsCatch.dir/catch_tests.cpp.o -o subgraphsCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../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 && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolMemTest1.dir/link.txt --verbose=1 -[ 36%] Built target subgraphsCatch -[ 36%] Linking CXX executable queryTestsCatch -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E 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queryTestsCatch make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 38%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.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 -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 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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 +[ 38%] Built target graphmolMemTest1 +[ 38%] Building CXX object Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o +[ 38%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MHFP.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/c++ -DAbbreviations_EXPORTS -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_ABBREVIATIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT 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-Wl,--dependency-file=CMakeFiles/moliteratorTestsCatch.dir/link.d CMakeFiles/moliteratorTestsCatch.dir/catch_moliterators.cpp.o -o moliteratorTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 /usr/lib/libCatch2.a ../../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' +[ 39%] Built target moliteratorTestsCatch [ 39%] 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 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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,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/moliteratorTestsCatch.dir/link.d CMakeFiles/moliteratorTestsCatch.dir/catch_moliterators.cpp.o -o moliteratorTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 /usr/lib/libCatch2.a ../../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' -[ 39%] Built target moliteratorTestsCatch [ 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 @@ -3956,52 +3992,16 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 39%] Building CXX object Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/test1.cpp.o [ 39%] Building CXX object Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/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/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 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 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 -/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' -[ 39%] Built target Abbreviations -make -f Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/build.make Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-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/Abbreviations/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/Abbreviations/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/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 -DrdReducedGraphs_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/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%] 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 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 39%] Building CXX object Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/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 -DrdAbbreviations_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/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o -MF CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o.d -o CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Abbreviations/Wrap/rdAbbreviations.cpp -[ 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 +[ 39%] Built target FragCatalog [ 39%] Linking CXX shared library ../../../lib/libRDKitForceFieldHelpers.so 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/MolAlign.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolAlign.so.1 -o ../../../lib/libRDKitMolAlign.so.1.2025.03.1 CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.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/MolAlign && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolAlign.so.1 ../../../lib/libRDKitMolAlign.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 39%] Built target MolAlign -make -f Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/depend -make -f 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../../../lib/libRDKitForceFieldHelpers.so.1 ../../../lib/libRDKitForceFieldHelpers.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' @@ -4022,71 +4022,80 @@ 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 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-Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DistGeom/CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o -MF CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o.d -o CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DistGeom/DistGeomUtils.cpp -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField/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 -DrdForceField_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/ForceField/Wrap/CMakeFiles/rdForceField.dir/ForceField.cpp.o -MF CMakeFiles/rdForceField.dir/ForceField.cpp.o.d -o CMakeFiles/rdForceField.dir/ForceField.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/Wrap/ForceField.cpp -[ 39%] Building CXX object Code/GraphMol/MolInteractionFields/CMakeFiles/MolInteractionFields.dir/MIFDescriptors.cpp.o -[ 39%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/DistViolationContribs.cpp.o -cd 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-Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolInteractionFields/CMakeFiles/MolInteractionFields.dir/MIFDescriptors.cpp.o -MF CMakeFiles/MolInteractionFields.dir/MIFDescriptors.cpp.o.d -o CMakeFiles/MolInteractionFields.dir/MIFDescriptors.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInteractionFields/MIFDescriptors.cpp -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DistGeom && /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 -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-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/DistGeom/CMakeFiles/DistGeometry.dir/DistViolationContribs.cpp.o -MF CMakeFiles/DistGeometry.dir/DistViolationContribs.cpp.o.d -o CMakeFiles/DistGeometry.dir/DistViolationContribs.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DistGeom/DistViolationContribs.cpp [ 40%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o -[ 40%] Building CXX object Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o -[ 40%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/ChiralViolationContribs.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/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 -DrdForceFieldHelpers_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/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 cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DistGeom && /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 -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-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/DistGeom/CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o -MF CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o.d -o CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DistGeom/TriangleSmooth.cpp +[ 40%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/ChiralViolationContribs.cpp.o +[ 40%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o +[ 40%] Building CXX object Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o +[ 40%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/DistViolationContribs.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DistGeom && /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 -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-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/DistGeom/CMakeFiles/DistGeometry.dir/ChiralViolationContribs.cpp.o -MF CMakeFiles/DistGeometry.dir/ChiralViolationContribs.cpp.o.d -o CMakeFiles/DistGeometry.dir/ChiralViolationContribs.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DistGeom/ChiralViolationContribs.cpp -[ 40%] 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 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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 -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' -[ 40%] Built target FragCatalog -[ 40%] 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 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 40%] 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' -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/Fingerprints/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/Fingerprints/Wrap 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Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o -MF CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o.d -o CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Abbreviations/Wrap/rdAbbreviations.cpp [ 40%] Linking CXX shared library ../../../lib/libRDKitMolChemicalFeatures.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/MolAlign.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolAlign.so.1 -o ../../../lib/libRDKitMolAlign.so.1.2025.03.1 CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 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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 -fPIC -MD -MT Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/Templates.cpp.o -MF CMakeFiles/Depictor.dir/Templates.cpp.o.d -o CMakeFiles/Depictor.dir/Templates.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Depictor/Templates.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/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 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' @@ -4097,36 +4106,39 @@ 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' +[ 40%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o [ 40%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o -cd 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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' [ 40%] Built target rdReducedGraphs +[ 40%] 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 [ 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 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/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' -/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' -[ 40%] Built target ForceFieldsCatch -[ 40%] 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 [ 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' @@ -4134,13 +4146,37 @@ 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 +[ 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 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 -/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 +[ 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' +[ 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' +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/Fingerprints/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/Fingerprints/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.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/Fingerprints/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/Fingerprints/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-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/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 41%] Building CXX object Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o +[ 41%] Building CXX object Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/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 -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 CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o.d -o CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/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 -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 +[ 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 testSLNParse +[ 41%] Built target ForceFieldsCatch [ 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 /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 @@ -4151,39 +4187,45 @@ make -f Code/DistGeom/CMakeFiles/testDistGeom.dir/build.make Code/DistGeom/CMakeFiles/testDistGeom.dir/depend make -f Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build.make Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-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/DistGeomHelpers.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 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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/DistGeomHelpers.dir/DependInfo.cmake "--color=" 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/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.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/DistGeom/CMakeFiles/testDistGeom.dir/build.make Code/DistGeom/CMakeFiles/testDistGeom.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]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 41%] Building CXX object Code/DistGeom/CMakeFiles/testDistGeom.dir/testDistGeom.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/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o -MF CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o.d -o CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/DistGeomHelpers/Embedder.cpp [ 41%] Building CXX object Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DistGeom.cpp.o [ 41%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o +[ 41%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o cd 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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 -fPIC -MD -MT Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o -MF CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o.d -o CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.cpp -[ 41%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o -[ 41%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.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 -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 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CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DistGeom/testDistGeom.cpp +[ 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++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 +[ 41%] Linking CXX shared module ../../../../rdkit/Chem/rdMolChemicalFeatures.so [ 41%] Linking CXX shared library ../../../lib/libRDKitMolInteractionFields.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 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++ -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 +/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 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 -[ 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 -[ 41%] Linking CXX executable smaTest1 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/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smaTest1.dir/link.txt --verbose=1 +[ 41%] Built target rdMolChemicalFeatures +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 41%] Built target MolInteractionFields make -f Code/GraphMol/MolInteractionFields/Wrap/CMakeFiles/rdMIF.dir/build.make Code/GraphMol/MolInteractionFields/Wrap/CMakeFiles/rdMIF.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' @@ -4193,37 +4235,40 @@ 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 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection 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-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 /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 +[ 41%] Linking CXX shared module ../../../rdkit/DistanceGeometry/DistGeom.so +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DistGeom/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeom.dir/link.txt --verbose=1 [ 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 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 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/DistGeom.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/DistanceGeometry/DistGeom.so CMakeFiles/DistGeom.dir/DistGeom.cpp.o ../../../lib/libRDKitDistGeometry.so.1.2025.03.1 ../../../lib/libRDKitRDBoost.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 /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 DistGeom +/usr/bin/c++ 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/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 rdAbbreviations /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 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-Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/hashfunctions.cpp.o -MF CMakeFiles/MolHash.dir/hashfunctions.cpp.o.d -o CMakeFiles/MolHash.dir/hashfunctions.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolHash/hashfunctions.cpp cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/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 -DIN_COORDGEN -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDepictor_EXPORTS -I/build/reproducible-path/rdkit-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/Depictor/Wrap/CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o -MF CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o.d -o CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Depictor/Wrap/rdDepictor.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 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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' -[ 42%] Built target rdAbbreviations -/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 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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 -[ 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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 43%] Built target DistGeomHelpers +[ 42%] Built target DistGeomHelpers +[ 42%] 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' -[ 43%] Built target MolHash +[ 42%] 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' -[ 43%] Building CXX object Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o +[ 42%] 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 +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/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 cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/External/INCHI-API && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDInchiLib.so.1.2025.03.1 ../../lib/libRDKitRDInchiLib.so.1 ../../lib/libRDKitRDInchiLib.so +[ 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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 43%] Built target RDInchiLib make -f External/INCHI-API/Wrap/CMakeFiles/rdinchi.dir/build.make External/INCHI-API/Wrap/CMakeFiles/rdinchi.dir/depend @@ -4312,6 +4350,9 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 43%] Building CXX object External/INCHI-API/Wrap/CMakeFiles/rdinchi.dir/pyInchi.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/External/INCHI-API/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 -Drdinchi_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 External/INCHI-API/Wrap/CMakeFiles/rdinchi.dir/pyInchi.cpp.o -MF CMakeFiles/rdinchi.dir/pyInchi.cpp.o.d -o CMakeFiles/rdinchi.dir/pyInchi.cpp.o -c /build/reproducible-path/rdkit-202503.1/External/INCHI-API/Wrap/pyInchi.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/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 +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 43%] Built target rdMIF [ 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 @@ -4322,11 +4363,6 @@ /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/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 -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 43%] Built target rdMIF [ 43%] Linking CXX shared module ../../../../rdkit/Chem/rdMolHash.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolHash.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/rdMolHash.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolHash.so CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o ../../../../lib/libRDKitMolHash.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.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/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.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 @@ -4344,68 +4380,68 @@ make[4]: Leaving 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 -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 -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 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-fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/TDTMolSupplier.cpp +[ 45%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/CMLWriter.cpp.o +[ 45%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/XYZFileParser.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 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Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MaeWriter.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/PDBWriter.cpp.o -MF CMakeFiles/FileParsers.dir/PDBWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/PDBWriter.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/PDBWriter.cpp +[ 45%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o +[ 46%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PNGParser.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/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 +[ 46%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o +[ 46%] 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 -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/XYZFileWriter.cpp.o -MF CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/XYZFileWriter.cpp +[ 46%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o +[ 46%] 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/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 +[ 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 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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/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 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 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/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 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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 /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' 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 -f Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolSGroupCatch.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/resMolSupplierTest.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/test-valgrind.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/depend -make -f Code/GraphMol/CMakeFiles/graphmolOrganometallicsCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolOrganometallicsCatch.dir/depend -make -f Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/depend make -f Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/depend -make -f Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/chiralityTestsCatch.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/graphmolTestsCatch.dir/DependInfo.cmake "--color=" -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/depend make -f Code/GraphMol/CMakeFiles/canonTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/canonTestsCatch.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/graphmolOrganometallicsCatch.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/pickleTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/pickleTestsCatch.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/graphmolSGroupCatch.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/graphmolOrganometallicsCatch.dir/DependInfo.cmake "--color=" 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/graphmolAdjustQueryCatch.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/chiralityTestsCatch.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-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/ChemReactions/CMakeFiles/ChemReactions.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.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/graphmolAdjustQueryCatch.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/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[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[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/SmilesParse/CMakeFiles/nontetrahedralCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/nontetrahedralCatch.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/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 -f Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/testDepictor.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/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/molopsTestsCatch.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/depend +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 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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/ChemReactions /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.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/nontetrahedralCatch.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/FileParsers/CMakeFiles/testAtropisomers.dir/build.make 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'/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 -f External/CoordGen/CMakeFiles/testCoordGen.dir/build.make External/CoordGen/CMakeFiles/testCoordGen.dir/build +make -f Code/GraphMol/FileParsers/CMakeFiles/testSquiggleDoubleBonds.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testSquiggleDoubleBonds.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/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/depictorCatch.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[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/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=" +make -f Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.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/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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/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/testMolSupplier.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-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/testGeneralFileReader.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-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 -f Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.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/testMolWriter.dir/DependInfo.cmake "--color=" +make -f 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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/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/testExtendedStereoParsing.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.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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'/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[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]: 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[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/GraphMol/CMakeFiles/molBundleTest.dir/build.make Code/GraphMol/CMakeFiles/molBundleTest.dir/build +make -f Code/GraphMol/CMakeFiles/testSGroup.dir/build.make 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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/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' -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 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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/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o -MF CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o.d -o CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/XYZFileParserCatchTest.cpp -[ 51%] Linking CXX executable testTplParser -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testTplParser.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/testTplParser.dir/link.d CMakeFiles/testTplParser.dir/testTpls.cpp.o -o testTplParser ../../../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 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-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/CDXMLParser.cpp.o -MF CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/CDXMLParser.cpp -[ 51%] 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 -[ 51%] 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 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 51%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.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 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Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o +[ 51%] 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 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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 -[ 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/molopsTestsCatch.dir/link.d CMakeFiles/molopsTestsCatch.dir/catch_molops.cpp.o -o molopsTestsCatch 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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/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o -MF CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o.d -o CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Enumerate/EnumerationPickler.cpp -[ 53%] Linking CXX executable nontetrahedralCatch -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/nontetrahedralCatch.dir/link.txt --verbose=1 -[ 53%] Linking CXX executable testSequence -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 /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 testSequence +[ 51%] Built target testSquiggleDoubleBonds make -f Code/GraphMol/FileParsers/CMakeFiles/v2FileParsersCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/v2FileParsersCatchTest.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 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CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -o graphmoltestPicklerGlobalSetting ../../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 ../../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 +/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 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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 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/XYZFileParserCatchTest.dir/link.d CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o -o XYZFileParserCatchTest ../../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' +[ 52%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/DaylightParser.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/DaylightParser.cpp.o -MF CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/DaylightParser.cpp +[ 52%] Built target XYZFileParserCatchTest make -f Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-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/testSubstructMatch.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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-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/Substruct/CMakeFiles/testSubstructMatch.dir/test1.cpp.o -MF CMakeFiles/testSubstructMatch.dir/test1.cpp.o.d -o CMakeFiles/testSubstructMatch.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Substruct/test1.cpp -[ 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 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../../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 +[ 52%] 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 -Wl,--dependency-file=CMakeFiles/molBundleTest.dir/link.d CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o -o molBundleTest ../../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 ../../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%] Built target resMolSupplierTest +[ 52%] Built target molBundleTest 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=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/build make[4]: Entering directory '/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 +[ 52%] 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 -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Substruct/catch_tests.cpp +[ 52%] Linking CXX executable testGeneralFileReader +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGeneralFileReader.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/testAtropisomers.dir/link.d CMakeFiles/testAtropisomers.dir/testAtropisomers.cpp.o -o testAtropisomers ../../../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/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 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/build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/DependInfo.cmake "--color=" +[ 52%] 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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 53%] Building CXX object 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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/FilterCatalog/CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o -MF CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o.d -o CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/filtercatalogtest.cpp -[ 54%] Linking CXX executable testExtendedStereoParsing -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testExtendedStereoParsing.dir/link.txt --verbose=1 -/usr/bin/c++ -g 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&& /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/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 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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/Fingerprints /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/DependInfo.cmake "--color=" -[ 55%] Built target multithreadedSupplierCatchTest make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 55%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolData3Ddescriptors.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 -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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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../../../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 +/usr/bin/c++ -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/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/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 56%] Built target v2MolSuppliers -[ 56%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/USRDescriptor.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 -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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/Descriptors/CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o -MF CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o.d -o CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/USRDescriptor.cpp +[ 54%] Built target testCoordGen make -f Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/build.make 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CXX object Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o +[ 54%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/catch_tests.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 -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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/Fingerprints/CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/catch_tests.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 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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 +[ 54%] Linking CXX executable v2FileParsersCatchTest +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/v2FileParsersCatchTest.dir/link.txt --verbose=1 +[ 54%] Linking CXX executable graphmolSGroupCatch +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolSGroupCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 /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' -[ 56%] Linking CXX executable molfileStereoCatchTest -[ 56%] Built target testMolWriter +[ 54%] Built target v2FileParsersCatchTest make -f Code/GraphMol/Fingerprints/CMakeFiles/fpGenTestCatch.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/fpGenTestCatch.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/Fingerprints /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints 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filterCatalogTest -[ 57%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/DCLV.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 -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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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-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/FragCatParams.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FragCatalog/Wrap/FragCatParams.cpp +[ 55%] Linking CXX executable testDepictor +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor && 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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 testPropertyLists make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-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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-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 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CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/ReactionPickler.cpp +[ 55%] 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 +[ 55%] 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 +/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' -[ 59%] Built target rdfragcatalog +/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 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molfileStereoCatchTest 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=" +[ 55%] Built target v2MolSuppliers make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f 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CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalFF.cpp -[ 60%] Linking CXX shared library ../../../lib/libRDKitChemReactions.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/ChemReactions.dir/link.txt --verbose=1 +[ 55%] 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 +[ 55%] Linking CXX executable multithreadedSupplierCatchTest +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/multithreadedSupplierCatchTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. 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CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o CMakeFiles/ChemReactions.dir/PNGParser.cpp.o CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 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cmake_symlink_library ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1 ../../../lib/libRDKitChemReactions.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/multithreadedSupplierCatchTest.dir/link.d CMakeFiles/multithreadedSupplierCatchTest.dir/multithreaded_supplier_catch.cpp.o -o multithreadedSupplierCatchTest ../../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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target forceFieldHelpersCatch make -f Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-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/FMCS /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 60%] 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-fcf-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/FMCS.cpp.o -MF CMakeFiles/FMCS.dir/FMCS.cpp.o.d -o CMakeFiles/FMCS.dir/FMCS.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/FMCS.cpp +[ 55%] Linking CXX executable testMolTransforms +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolTransforms.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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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-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/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FragCatalog/Wrap/FragFPGenerator.cpp +[ 55%] Built target testMolTransforms make -f 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 61%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o +[ 56%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolHash && /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/MolHash/CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o -MF CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o.d -o CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolHash/catch_tests.cpp -[ 61%] 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 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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/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 -[ 63%] Linking CXX executable testMMFFForceFieldHelpersMultiThread +[ 57%] Linking CXX executable testMMFFForceFieldHelpersMultiThread 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/MolInterchange/CMakeFiles/molInterchangeTest1.dir/test1.cpp.o -MF CMakeFiles/molInterchangeTest1.dir/test1.cpp.o.d -o CMakeFiles/molInterchangeTest1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInterchange/test1.cpp -[ 64%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawShape.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 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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 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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 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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[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/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 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-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 Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/lap_a_la_scipy.cpp.o -MF CMakeFiles/RascalMCES.dir/lap_a_la_scipy.cpp.o.d -o CMakeFiles/RascalMCES.dir/lap_a_la_scipy.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/lap_a_la_scipy.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/MolProcessing.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolProcessing.so.1 -o ../../../lib/libRDKitMolProcessing.so.1.2025.03.1 CMakeFiles/MolProcessing.dir/MolProcessing.cpp.o ../../../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 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make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 70%] Built target testUFFForceFieldHelpers -[ 70%] 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 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executable molInterchangeCatchTest +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/molInterchangeCatchTest.dir/link.txt --verbose=1 +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 -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 65%] Built target testMMPA +[ 65%] Linking CXX shared module ../../../../rdkit/Chem/rdMMPA.so +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMMPA.dir/link.txt --verbose=1 +[ 65%] Linking CXX executable testMIF +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInteractionFields && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMIF.dir/link.txt --verbose=1 +[ 65%] Linking CXX executable testDistGeomHelpers +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDistGeomHelpers.dir/link.txt --verbose=1 +/usr/bin/c++ -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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../../../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 +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 65%] Built target testMIF +/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 +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 65%] Built target testDistGeomHelpers +[ 65%] Linking CXX executable testMolProcessing +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolProcessing.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/testMolProcessing.dir/link.d CMakeFiles/testMolProcessing.dir/processing_tests.cpp.o -o testMolProcessing ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolProcessing.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../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/libRDKitFingerprints.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 ../../../lib/libRDKitRDStreams.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' +[ 65%] Linking CXX executable fileParsersCatchTest +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileParsersCatchTest.dir/link.txt --verbose=1 +[ 65%] Built target testMolProcessing +/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/fileParsersCatchTest.dir/link.d CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o -o fileParsersCatchTest ../../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' +[ 65%] Built target fileParsersCatchTest +[ 65%] 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 +/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/graphmolTestsCatch.dir/link.d CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o -o graphmolTestsCatch ../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/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' +[ 65%] Built target graphmolTestsCatch +[ 66%] 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 -Wformat -Werror=format-security -fcf-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/FMCS.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFMCS.so.1 -o ../../../lib/libRDKitFMCS.so.1.2025.03.1 CMakeFiles/FMCS.dir/FMCS.cpp.o CMakeFiles/FMCS.dir/Seed.cpp.o CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../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 +cd /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' +[ 66%] Built target FMCS +make -f Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/depend +make -f Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build.make Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/depend +make -f Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build.make Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +cd 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/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.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/FMCS/Test /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.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[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 -f Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build +make -f Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build.make Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +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' -[ 70%] Built target trajectoryTest +[ 66%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o +[ 66%] 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 -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/FMCS/Test/CMakeFiles/FMCStest.dir/testFMCS.cpp.o -MF 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+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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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Deprotect/Deprotect.cpp +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /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 -DMolEnumerator_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLENUMERATOR_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-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/MolEnumerator/CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o -MF CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o.d -o CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/PositionVariation.cpp +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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-Wformat -Werror=format-security -fcf-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/MarvinParse/CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o -MF CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o.d -o CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MarvinParse/MarvinDefs.cpp +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /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 -DMolEnumerator_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLENUMERATOR_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED 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-DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolEnumerator_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLENUMERATOR_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-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 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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 -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/ChemReactions/CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o -MF CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o.d -o CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/testReactionFingerprints.cpp 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 -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDeprotect.so.1.2025.03.1 ../../../lib/libRDKitDeprotect.so.1 ../../../lib/libRDKitDeprotect.so +[ 73%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawText.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 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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/Wrap/CMakeFiles/rdmolops.dir/MolOps.cpp.o -MF CMakeFiles/rdmolops.dir/MolOps.cpp.o.d -o CMakeFiles/rdmolops.dir/MolOps.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/MolOps.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 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Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o -MF CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o.d -o CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/ChiralityOps.cpp +[ 74%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Charge.cpp.o +[ 74%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Validate.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 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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/Tautomer.cpp.o -MF CMakeFiles/MolStandardize.dir/Tautomer.cpp.o.d -o CMakeFiles/MolStandardize.dir/Tautomer.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Tautomer.cpp +[ 74%] 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 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]', @@ -5704,276 +5903,158 @@ /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))); | ^ -/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 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../../../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 +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDeprotect.so.1.2025.03.1 ../../../lib/libRDKitDeprotect.so.1 ../../../lib/libRDKitDeprotect.so +[ 75%] Linking CXX executable testReactionFingerprints +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReactionFingerprints.dir/link.txt --verbose=1 +[ 75%] 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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 73%] Built target testFingerprints -[ 73%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Charge.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 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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 -[ 73%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Fragment.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/Fragment.cpp.o -MF CMakeFiles/MolStandardize.dir/Fragment.cpp.o.d -o CMakeFiles/MolStandardize.dir/Fragment.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Fragment.cpp -[ 73%] 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 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../../../lib/libRDKitMolProcessing.so.1.2025.03.1 CMakeFiles/MolProcessing.dir/MolProcessing.cpp.o ../../../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 -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 -/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 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-fcf-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/RascalMCES.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRascalMCES.so.1 -o ../../../lib/libRDKitRascalMCES.so.1.2025.03.1 CMakeFiles/RascalMCES.dir/RascalMCES.cpp.o CMakeFiles/RascalMCES.dir/RascalCluster.cpp.o CMakeFiles/RascalMCES.dir/RascalButinaCluster.cpp.o CMakeFiles/RascalMCES.dir/lap_a_la_scipy.cpp.o CMakeFiles/RascalMCES.dir/PartitionSet.cpp.o CMakeFiles/RascalMCES.dir/RascalResult.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/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 ../../../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 +[ 75%] Built target testReactionFingerprints +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 -f Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/build.make Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.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/Deprotect/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/Deprotect/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/DependInfo.cmake "--color=" -[ 73%] Linking CXX executable testDistGeomHelpers -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDistGeomHelpers.dir/link.txt --verbose=1 -[ 73%] Linking CXX shared library ../../../lib/libRDKitMolEnumerator.so 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Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o -MF CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o.d -o CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Deprotect/Wrap/rdDeprotect.cpp -[ 74%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.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 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../../../lib/libRDKitRascalMCES.so +[ 76%] Linking CXX shared library ../../../lib/libRDKitMolEnumerator.so +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolEnumerator.dir/link.txt --verbose=1 +[ 76%] 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 -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 ../../../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 /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/MolEnumerator && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1 ../../../lib/libRDKitMolEnumerator.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 77%] 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 -f Code/GraphMol/RascalMCES/Wrap/CMakeFiles/rdRascalMCES.dir/build.make 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/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=" 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/RascalMCES/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/RascalMCES/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES/Wrap/CMakeFiles/rdRascalMCES.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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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 -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/RascalMCES/CMakeFiles/testRascalCluster.dir/mces_cluster_catch.cpp.o -MF CMakeFiles/testRascalCluster.dir/mces_cluster_catch.cpp.o.d -o CMakeFiles/testRascalCluster.dir/mces_cluster_catch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/mces_cluster_catch.cpp -cd 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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 +[ 77%] 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 -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolEnumerator_EXPORTS -I/build/reproducible-path/rdkit-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/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o -MF CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o.d -o CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/Wrap/rdMolEnumerator.cpp +[ 77%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /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/MolEnumerator/CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -MF CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o.d -o CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/enumerator_catch.cpp +[ 77%] Linking CXX executable testRascalCluster +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRascalCluster.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/testRascalCluster.dir/link.d CMakeFiles/testRascalCluster.dir/mces_cluster_catch.cpp.o -o testRascalCluster ../../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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/RascalMCES/Wrap/CMakeFiles/rdRascalMCES.dir/build.make Code/GraphMol/RascalMCES/Wrap/CMakeFiles/rdRascalMCES.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 77%] Building CXX object Code/GraphMol/RascalMCES/Wrap/CMakeFiles/rdRascalMCES.dir/rdRascalMCES.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES/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 -DrdRascalMCES_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/RascalMCES/Wrap/CMakeFiles/rdRascalMCES.dir/rdRascalMCES.cpp.o -MF CMakeFiles/rdRascalMCES.dir/rdRascalMCES.cpp.o.d -o CMakeFiles/rdRascalMCES.dir/rdRascalMCES.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/Wrap/rdRascalMCES.cpp -[ 77%] Linking CXX shared module ../../../../rdkit/Chem/rdMMPA.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMMPA.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 +[ 77%] Built target testRascalCluster +[ 77%] Linking CXX executable deprotectTest +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect && /usr/bin/cmake -E cmake_link_script CMakeFiles/deprotectTest.dir/link.txt --verbose=1 +[ 77%] 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 +/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/deprotectTest.dir/link.d CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o -o deprotectTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitDeprotect.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 ../../../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' -[ 77%] Linking CXX executable testMolProcessing -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolProcessing.dir/link.txt --verbose=1 -[ 77%] Built target rdMMPA +[ 77%] Built target deprotectTest +/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[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 77%] Built target rdFMCS +[ 77%] Linking CXX executable graphmolMolOpsTest +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolMolOpsTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/graphmolMolOpsTest.dir/link.d CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -o graphmolMolOpsTest ../../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' +[ 77%] Built target graphmolMolOpsTest +[ 77%] Linking CXX shared library ../../../lib/libRDKitDescriptors.so +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/Descriptors.dir/link.txt --verbose=1 +[ 77%] Linking CXX shared module ../../../../rdkit/Chem/rdRascalMCES.so +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdRascalMCES.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/rdRascalMCES.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdRascalMCES.so CMakeFiles/rdRascalMCES.dir/rdRascalMCES.cpp.o ../../../../lib/libRDKitRascalMCES.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 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 77%] Built target rdRascalMCES +[ 77%] Linking CXX shared library ../../../lib/libRDKitMolStandardize.so +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolStandardize.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/Descriptors.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDescriptors.so.1 -o ../../../lib/libRDKitDescriptors.so.1.2025.03.1 CMakeFiles/Descriptors.dir/Crippen.cpp.o CMakeFiles/Descriptors.dir/BCUT.cpp.o CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o CMakeFiles/Descriptors.dir/MolSurf.cpp.o CMakeFiles/Descriptors.dir/Lipinski.cpp.o CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o CMakeFiles/Descriptors.dir/MQN.cpp.o CMakeFiles/Descriptors.dir/Property.cpp.o CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o CMakeFiles/Descriptors.dir/AtomFeat.cpp.o CMakeFiles/Descriptors.dir/OxidationNumbers.cpp.o CMakeFiles/Descriptors.dir/DCLV.cpp.o CMakeFiles/Descriptors.dir/EEM.cpp.o CMakeFiles/Descriptors.dir/PBF.cpp.o CMakeFiles/Descriptors.dir/PMI.cpp.o CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o CMakeFiles/Descriptors.dir/RDF.cpp.o CMakeFiles/Descriptors.dir/MORSE.cpp.o CMakeFiles/Descriptors.dir/GETAWAY.cpp.o CMakeFiles/Descriptors.dir/WHIM.cpp.o CMakeFiles/Descriptors.dir/CoulombMat.cpp.o ../../../lib/libRDKitPartialCharges.so.1.2025.03.1 ../../../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/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/libRDKitAlignment.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 cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDescriptors.so.1.2025.03.1 ../../../lib/libRDKitDescriptors.so.1 ../../../lib/libRDKitDescriptors.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/testMolProcessing.dir/link.d CMakeFiles/testMolProcessing.dir/processing_tests.cpp.o -o testMolProcessing ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolProcessing.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../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/libRDKitFingerprints.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 ../../../lib/libRDKitRDStreams.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' -[ 77%] Linking CXX executable testEnumeration -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testEnumeration.dir/link.txt --verbose=1 -[ 77%] Built target testMolProcessing [ 77%] Built target Descriptors make -f Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/depend make -f Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/depend @@ -5982,603 +6063,558 @@ make -f Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd 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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 /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/testEEM.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/depend +make -f Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-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 /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/testPBF.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/Descriptors/CMakeFiles/testDescriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/build -make -f Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f 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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 /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/testRDF.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.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/Descriptors/CMakeFiles/testATF.dir/build.make 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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/Descriptors /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/Descriptors/CMakeFiles/descriptorsTestCatch.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/descriptorsTestCatch.dir/depend +make -f Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/build.make Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-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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/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/testGETAWAY.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -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 -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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/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 -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 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/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 -f Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 80%] Built target MolDraw2D -make -f Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-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 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/testWHIM.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/MolStandardize.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolStandardize.so.1 -o ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 CMakeFiles/MolStandardize.dir/Pipeline.cpp.o CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o CMakeFiles/MolStandardize.dir/Metal.cpp.o CMakeFiles/MolStandardize.dir/Normalize.cpp.o CMakeFiles/MolStandardize.dir/Validate.cpp.o CMakeFiles/MolStandardize.dir/Charge.cpp.o CMakeFiles/MolStandardize.dir/Tautomer.cpp.o CMakeFiles/MolStandardize.dir/Fragment.cpp.o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../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 ../../../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/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%] Linking CXX executable testRascalCluster -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRascalCluster.dir/link.txt --verbose=1 [ 80%] 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 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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/molStandardizeSmallTest.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/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/molFragmentTest.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-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 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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[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]: 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/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[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 && /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 -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build make -f Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build.make 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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[4]: Entering 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/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/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/build +make -f 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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 +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMarvinParser.so.1.2025.03.1 ../../../lib/libRDKitMarvinParser.so.1 ../../../lib/libRDKitMarvinParser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 83%] Built target testCoulombMat -/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/testWHIM.dir/link.d CMakeFiles/testWHIM.dir/testWHIM.cpp.o -o testWHIM ../../../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 +[ 83%] Built target MarvinParser +make -f Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-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/cxsmilesTest.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 83%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o +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 -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/SmilesParse/CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o -MF CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o.d -o CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse/cxsmiles_test.cpp +[ 83%] 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 CMakeFiles/testRDF.dir/testRDF.cpp.o -o testRDF ../../../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 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Code/GraphMol/MarvinParse/CMakeFiles/testMrvToMol.dir/depend +/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/MolDraw2D.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolDraw2D.so.1 -o ../../../lib/libRDKitMolDraw2D.so.1.2025.03.1 CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o CMakeFiles/MolDraw2D.dir/DrawMolMCHCircleAndLine.cpp.o 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../../../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]: 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/MarvinParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/CMakeFiles/testMrvToMol.dir/DependInfo.cmake "--color=" [ 83%] 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 -[ 83%] Linking CXX shared module ../../../../rdkit/Chem/rdMolEnumerator.so -cd 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../../../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 +[ 83%] Linking CXX executable testBCUT +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testBCUT.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 83%] Built target testAUTOCORR3D -/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 ../../../../rdkit/Chem/rdMolEnumerator.so CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o ../../../../lib/libRDKitMolEnumerator.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/libRDKitFilterCatalog.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 -f Code/GraphMol/MarvinParse/CMakeFiles/testMrvToMol.dir/build.make Code/GraphMol/MarvinParse/CMakeFiles/testMrvToMol.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 83%] Linking CXX executable testMORSE +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMORSE.dir/link.txt --verbose=1 +[ 83%] Building CXX object Code/GraphMol/MarvinParse/CMakeFiles/testMrvToMol.dir/testMrvToMol.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse && /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 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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' -[ 83%] Built target rdRascalMCES -/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/testFMCS.dir/link.d CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -o testFMCS ../../../lib/libRDKitFMCS.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 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cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/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/ChemReactions/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 84%] 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 -[ 84%] Built target testFMCS -/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 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testBCUT ../../../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 +/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/testMORSE.dir/link.d CMakeFiles/testMORSE.dir/testMORSE.cpp.o -o testMORSE ../../../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' -[ 84%] Built target test3D -[ 84%] Linking CXX executable graphmolMolOpsTest -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolMolOpsTest.dir/link.txt --verbose=1 -[ 84%] Linking CXX executable moldraw2DRxnTest1 -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DRxnTest1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/graphmolMolOpsTest.dir/link.d CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -o graphmolMolOpsTest ../../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' -[ 84%] Built target graphmolMolOpsTest -/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/moldraw2DRxnTest1.dir/link.d CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -o moldraw2DRxnTest1 ../../../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 +[ 84%] Building CXX object Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/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 -DrdChemReactions_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/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o -MF CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o.d -o CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp +[ 84%] Built target testBCUT +/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 -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.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/moldraw2DTest1.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 84%] Built target moldraw2DRxnTest1 -[ 84%] Linking CXX shared library ../../../lib/libRDKitMarvinParser.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/MarvinParser.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/MarvinParser.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMarvinParser.so.1 -o ../../../lib/libRDKitMarvinParser.so.1.2025.03.1 CMakeFiles/MarvinParser.dir/MarvinParser.cpp.o CMakeFiles/MarvinParser.dir/MarvinWriter.cpp.o CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o ../../../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 -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMarvinParser.so.1.2025.03.1 ../../../lib/libRDKitMarvinParser.so.1 ../../../lib/libRDKitMarvinParser.so +[ 84%] Built target testMORSE +make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/depend make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 84%] Built target MarvinParser -make -f Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/depend -make -f Code/GraphMol/MarvinParse/CMakeFiles/testMrvToMol.dir/build.make Code/GraphMol/MarvinParse/CMakeFiles/testMrvToMol.dir/depend -make -f Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/build.make Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/depend -make -f Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/build.make Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/depend -make[4]: Entering directory '/build/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/cxsmilesTest.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/MarvinParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/CMakeFiles/testMrvToMol.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/GenericGroups /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/DependInfo.cmake "--color=" +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 -f Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.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/ChemReactions/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/ChemReactions/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/depend -make -f Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.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/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]: 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/CIPLabeler /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/DependInfo.cmake "--color=" +[ 84%] Built target testAUTOCORR3D +make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-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 /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdchem.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/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/moldraw2DRxnTest1.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 84%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/test1.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 -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD 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-fcf-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/molNormalizeTest.dir/link.d CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o -o molNormalizeTest ../../../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 +[ 84%] Built target testRDFcustom make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 85%] Built target molNormalizeTest -[ 85%] 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 -[ 86%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeWriter.cpp.o +[ 84%] Built target molFragmentTest +[ 84%] 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 +[ 84%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ 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-fcf-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/MaeMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/MaeMolSupplier.cpp +[ 84%] Built target molNormalizeTest +[ 85%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeWriter.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 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-Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/SDMolSupplier.cpp +[ 86%] 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/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' -[ 86%] Linking CXX executable testMolEnumerator -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolEnumerator.dir/link.txt --verbose=1 -[ 86%] Built target descriptorsTestCatch -[ 86%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPMol.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 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cmake_symlink_library ../../../lib/libRDKitO3AAlign.so.1.2025.03.1 ../../../lib/libRDKitO3AAlign.so.1 ../../../lib/libRDKitO3AAlign.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/ScaffoldNetwork.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitScaffoldNetwork.so.1 -o ../../../lib/libRDKitScaffoldNetwork.so.1.2025.03.1 CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o ../../../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 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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/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o -MF CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/CIPLabeler.cpp +[ 88%] Linking CXX executable molStandardizeTest +[ 88%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Mol.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap 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Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MonomerInfo.cpp.o -MF CMakeFiles/rdchem.dir/MonomerInfo.cpp.o.d -o CMakeFiles/rdchem.dir/MonomerInfo.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/MonomerInfo.cpp -[ 89%] Linking CXX executable molStandardizeTest -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizeTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/molStandardizeTest.dir/link.d CMakeFiles/molStandardizeTest.dir/test1.cpp.o -o molStandardizeTest ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 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Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/ResonanceMolSupplier.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/ResonanceMolSupplier.cpp.o -MF CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o.d -o CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/ResonanceMolSupplier.cpp -[ 89%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDWriter.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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-MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o -MF CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o.d -o CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/SDWriter.cpp -[ 89%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Node.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/Node.cpp.o -MF CMakeFiles/testCIPLabeler.dir/Node.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/Node.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/Node.cpp -[ 89%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MolBundle.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 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/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/TDTWriter.cpp.o -MF CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o.d -o CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/TDTWriter.cpp make -f Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/build.make Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.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 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-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 [ 89%] Building CXX object Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/XQMol.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 -DGeneralizedSubstruct_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GENERALIZEDSUBSTRUCT_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/XQMol.cpp.o -MF CMakeFiles/GeneralizedSubstruct.dir/XQMol.cpp.o.d -o CMakeFiles/GeneralizedSubstruct.dir/XQMol.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/GeneralizedSubstruct/XQMol.cpp -[ 89%] Building CXX object Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/TextIO.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 -DGeneralizedSubstruct_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GENERALIZEDSUBSTRUCT_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/TextIO.cpp.o -MF CMakeFiles/GeneralizedSubstruct.dir/TextIO.cpp.o.d -o CMakeFiles/GeneralizedSubstruct.dir/TextIO.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/GeneralizedSubstruct/TextIO.cpp -[ 89%] Linking CXX shared module ../../../rdkit/Chem/rdmolops.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdmolops.dir/link.txt --verbose=1 +[ 89%] Linking CXX executable molStandardizePipelineTest +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizePipelineTest.dir/link.txt --verbose=1 +[ 89%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Mancude.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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../../../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' +[ 89%] Built target molStandardizePipelineTest +[ 89%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Digraph.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/Digraph.cpp.o -MF CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/Digraph.cpp +[ 89%] Linking CXX executable molTautomerTest +cd 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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/Wrap/CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o -MF CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o.d -o CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/SmilesWriter.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/molTautomerTest.dir/link.d CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o -o molTautomerTest ../../../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]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 89%] Built target molTautomerTest make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd 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Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecompData.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=. -fstack-protector-strong 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-fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupData.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupData.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupData.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition/RGroupData.cpp +[ 89%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MonomerInfo.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/MonomerInfo.cpp.o -MF CMakeFiles/rdchem.dir/MonomerInfo.cpp.o.d -o CMakeFiles/rdchem.dir/MonomerInfo.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/MonomerInfo.cpp [ 89%] Linking CXX executable testMrvToMol cd 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--verbose=1 +[ 89%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/PDBWriter.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/PDBWriter.cpp.o -MF CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o.d -o CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/PDBWriter.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/testMrvToMol.dir/link.d CMakeFiles/testMrvToMol.dir/testMrvToMol.cpp.o -o testMrvToMol ../../../lib/libRDKitMarvinParser.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 /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' -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/configs/Configuration.cpp.o -MF CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/configs/Configuration.cpp -[ 89%] Built target testMrvToMol -[ 89%] Building CXX object 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 -fcf-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/configs/Sp2Bond.cpp.o -MF CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/configs/Sp2Bond.cpp -[ 89%] Linking CXX executable 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 -/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/molTautomerTest.dir/link.d CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o -o molTautomerTest ../../../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 +/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/testGenericGroups.dir/link.d CMakeFiles/testGenericGroups.dir/generic_tests.cpp.o -o testGenericGroups ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMarvinParser.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../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' -[ 89%] Built target molTautomerTest -[ 89%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/StereoGroup.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/StereoGroup.cpp.o -MF CMakeFiles/rdchem.dir/StereoGroup.cpp.o.d -o CMakeFiles/rdchem.dir/StereoGroup.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/StereoGroup.cpp -[ 89%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/SubstanceGroup.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/SubstanceGroup.cpp.o -MF CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o.d -o CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/SubstanceGroup.cpp -[ 89%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Chirality.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/Chirality.cpp.o -MF CMakeFiles/rdchem.dir/Chirality.cpp.o.d -o CMakeFiles/rdchem.dir/Chirality.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/Chirality.cpp -[ 89%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupUtils.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=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition/RGroupUtils.cpp +[ 89%] 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 +[ 89%] Built target testMrvToMol make -f Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-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/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/ScaffoldNetwork/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/DependInfo.cmake "--color=" @@ -6679,6 +6692,30 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 89%] Building CXX object Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/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 -DrdScaffoldNetwork_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/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o -MF CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o.d -o CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ScaffoldNetwork/Wrap/rdScaffoldNetwork.cpp +[ 89%] Built target testGenericGroups +[ 89%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Sort.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/Sort.cpp.o -MF CMakeFiles/testCIPLabeler.dir/Sort.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/Sort.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/Sort.cpp +[ 89%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/ResonanceMolSupplier.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 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Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o -MF CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o.d -o CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/ResonanceMolSupplier.cpp +[ 89%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Configuration.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/configs/Configuration.cpp.o -MF CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/configs/Configuration.cpp +[ 89%] Linking CXX executable tautomerQueryTestCatch +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_link_script 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/configs/Tetrahedral.cpp +[ 89%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.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/MultithreadedSmilesMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/MultithreadedSmilesMolSupplier.cpp +[ 89%] Building CXX object Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/TextIO.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 -fPIC -MD -MT Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/TextIO.cpp.o -MF CMakeFiles/GeneralizedSubstruct.dir/TextIO.cpp.o.d -o CMakeFiles/GeneralizedSubstruct.dir/TextIO.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/GeneralizedSubstruct/TextIO.cpp +[ 89%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/AtropisomerBond.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/configs/AtropisomerBond.cpp.o -MF CMakeFiles/testCIPLabeler.dir/configs/AtropisomerBond.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/configs/AtropisomerBond.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/configs/AtropisomerBond.cpp +[ 89%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.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/MultithreadedSDMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/MultithreadedSDMolSupplier.cpp 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, @@ -6707,6 +6744,8 @@ /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]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 89%] Linking CXX executable molStandardizeCatchTest +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizeCatchTest.dir/link.txt --verbose=1 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] @@ -6726,85 +6765,102 @@ /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]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 /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/TautomerQuery /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery 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Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 89%] Built target testO3AAlign -[ 89%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.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 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Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 90%] Built target rdTautomerQuery [ 90%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule2.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 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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++ -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' -[ 91%] Built target rdMolStandardize -[ 92%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.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 -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/rules/SequenceRule.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/SequenceRule.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/SequenceRule.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/rules/SequenceRule.cpp -[ 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 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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/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 +[ 92%] Built target rdMolAlign +[ 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 CMakeFiles/testCIPLabeler.dir/rules/Rule5.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule5New.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule6.cpp.o CMakeFiles/testCIPLabeler.dir/rules/SequenceRule.cpp.o -o testCIPLabeler ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMarvinParser.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../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' +[ 92%] Built target testCIPLabeler +[ 92%] 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 +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 92%] Built target rdMolDescriptors [ 92%] Linking CXX shared library ../../../lib/libRDKitGeneralizedSubstruct.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/GeneralizedSubstruct.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/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 ../../../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 @@ -6814,83 +6870,81 @@ make -f Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/depend make -f Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/depend make -f Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/build.make Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/depend -make -f Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/build.make Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/depend -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/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[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/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/build.make Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/depend +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 /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.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/GeneralizedSubstruct/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/GeneralizedSubstruct/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.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/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[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/PgSQL/rdkit /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/PgSQL/rdkit /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/build.make Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.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/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build make -f Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/build.make Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/build -make -f Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/build.make Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.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]: 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]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 92%] Building CXX object Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o -[ 92%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o +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/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/build.make Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/build +[ 92%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/Synthon.cpp.o [ 92%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpace.cpp.o [ 92%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSet.cpp.o -[ 92%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bfp_op.c.o -[ 92%] Building CXX object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/adapter.cpp.o -[ 92%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o -[ 92%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/Synthon.cpp.o -[ 92%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/cache.c.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 -DRDKIT_SUBSTRUCTLIBRARY_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-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 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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/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSet.cpp.o -MF CMakeFiles/SynthonSpaceSearch.dir/SynthonSet.cpp.o.d -o CMakeFiles/SynthonSpaceSearch.dir/SynthonSet.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/SynthonSet.cpp -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB 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-Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/adapter.cpp.o -MF CMakeFiles/rdkit.dir/adapter.cpp.o.d -o CMakeFiles/rdkit.dir/adapter.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/adapter.cpp -cd /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 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/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/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/cache.c.o -MF CMakeFiles/rdkit.dir/cache.c.o.d -o CMakeFiles/rdkit.dir/cache.c.o -c /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/cache.c -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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-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/bfp_op.c.o -MF CMakeFiles/rdkit.dir/bfp_op.c.o.d -o CMakeFiles/rdkit.dir/bfp_op.c.o -c /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/bfp_op.c [ 93%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/low_gist.c.o -[ 93%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearcher.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && 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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/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 @@ -6899,29 +6953,18 @@ 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/rxn_op.c.o -MF CMakeFiles/rdkit.dir/rxn_op.c.o.d -o CMakeFiles/rdkit.dir/rxn_op.c.o -c /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 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/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++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/testCIPLabeler.dir/rules/Rule5.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule5New.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule6.cpp.o CMakeFiles/testCIPLabeler.dir/rules/SequenceRule.cpp.o -o testCIPLabeler ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMarvinParser.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../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' -[ 95%] Built target testCIPLabeler -/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 -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/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 -[ 95%] Linking CXX executable tautomerQueryTestCatch -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_link_script CMakeFiles/tautomerQueryTestCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -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' -[ 95%] Built target rdMolAlign -/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/tautomerQueryTestCatch.dir/link.d CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o -o tautomerQueryTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../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 +[ 95%] Linking CXX executable testScaffoldNetwork +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_link_script CMakeFiles/testScaffoldNetwork.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/testScaffoldNetwork.dir/link.d CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o -o testScaffoldNetwork ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitScaffoldNetwork.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../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/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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 95%] Built target tautomerQueryTestCatch -[ 95%] 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 -/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 +[ 95%] Built target testScaffoldNetwork +[ 96%] 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 -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdScaffoldNetwork.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/Scaffolds/rdScaffoldNetwork.so CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o ../../../../lib/libRDKitScaffoldNetwork.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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 95%] Built target rdMolDraw2D +[ 96%] Built target rdScaffoldNetwork +[ 96%] 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 /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, @@ -6932,130 +6975,143 @@ /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/adapter.cpp:1637:44: warning: unused parameter 'bitFlags' [-Wunused-parameter] 1637 | unsigned int bitFlags) { | ~~~~~~~~~~~~~^~~~~~~~ -[ 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 -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 96%] 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 -[ 96%] Built target rdTautomerQuery -/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/rdScaffoldNetwork.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/Scaffolds/rdScaffoldNetwork.so CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o ../../../../lib/libRDKitScaffoldNetwork.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 -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 96%] Built target rdScaffoldNetwork -[ 96%] Linking CXX executable testScaffoldNetwork -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_link_script CMakeFiles/testScaffoldNetwork.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/testScaffoldNetwork.dir/link.d CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o -o testScaffoldNetwork ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitScaffoldNetwork.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../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/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/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' -[ 96%] Built target testScaffoldNetwork +[ 96%] Built target moldraw2DTest1 [ 97%] 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 -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' [ 97%] Built target rdmolfiles +[ 97%] Linking CXX 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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 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/sql /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/PgSQL/rdkit/sql 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/data /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/PgSQL/rdkit/data 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%] 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 +[ 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%] Built target rdkit /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 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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 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdChemReactions.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdChemReactions.so CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o ../../../../lib/libRDKitMarvinParser.so.1.2025.03.1 ../../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.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 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 97%] Built target rdChemReactions -[ 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++ -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 -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 97%] Built target rdchem -[ 97%] Linking CXX executable testReaction -cd 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-fcf-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 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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 -[ 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 /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' -/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 [ 97%] Built target gaExample -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 97%] Built target testRGroupDecompInternals [ 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 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/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 module ../../../../rdkit/Chem/rdRGroupDecomposition.so +[ 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 +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++ -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 rdRGroupDecomposition /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 -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/depend make -f Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/depend make[4]: Entering directory '/build/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[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[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=" 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/substructLibraryCatchTest.dir/DependInfo.cmake "--color=" @@ -7064,55 +7120,35 @@ 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/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.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/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceRascalSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceRascalSearch.dir/build +make -f Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/build make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build 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 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Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -MF CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o.d -o CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SubstructLibrary/Wrap/rdSubstructLibrary.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/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=" -cd 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-Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -MF CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o.d -o CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SubstructLibrary/substructLibraryTest.cpp -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 -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 -DrdSubstructLibrary_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/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 +[ 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 -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 -DrdSubstructLibrary_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/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 -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 -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/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceRascalSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceRascalSearch.dir/build -make -f Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.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' -[ 97%] 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 && /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/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceRascalSearch.dir/rascal_search_catch_tests.cpp.o -MF CMakeFiles/testSynthonSpaceRascalSearch.dir/rascal_search_catch_tests.cpp.o.d -o CMakeFiles/testSynthonSpaceRascalSearch.dir/rascal_search_catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/rascal_search_catch_tests.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 -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/substructLibraryTest.dir/substructLibraryTest.cpp.o -MF CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o.d -o CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SubstructLibrary/substructLibraryTest.cpp +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 -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 -DrdSubstructLibrary_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/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -MF CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o.d -o CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SubstructLibrary/Wrap/rdSubstructLibrary.cpp [ 98%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o -make[4]: Leaving 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 && /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/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 -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o -MF CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o.d -o CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/substructure_search_catch_tests.cpp -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' -[ 98%] 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 [ 98%] 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 -[ 98%] 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/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' [ 98%] Built target rgroupCatchTests -/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' -[ 98%] Built target rdRGroupDecomposition [ 98%] 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 ../../../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/libRDKitEigenSolvers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcairo.so /usr/lib/x86_64-linux-gnu/libfreetype.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 @@ -7125,31 +7161,31 @@ [ 98%] Built target testSynthonSpaceRascalSearch [ 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 -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 98%] Built target substructLibraryCatchTest [ 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 /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 +/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 substructLibraryTest -[ 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: 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' -/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 substructLibraryCatchTest +[ 99%] Built target substructLibraryTest [ 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 -[ 99%] Built target testSynthonSpaceSubstructureSearch /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 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 [ 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 +/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' /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++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 [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 -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdSubstructLibrary.so CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o ../../../../lib/libRDKitSubstructLibrary.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.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/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/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... Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol +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/MolTransforms +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Substruct +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/Abbreviations Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolCatalog -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/MolEnumerator +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/FileParsers +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/TautomerQuery +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FragCatalog +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/MolHash +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Subgraphs +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/GeneralizedSubstruct -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolAlign -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/MolProcessing Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse -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/FragCatalog +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolAlign +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/Trajectory +Searching for files in directory 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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: @@ -15672,401 +15696,41 @@ 1: 2 5 1 0 1: M END 1: -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: [00:24:56] Testing Github940: property dictionaries leaking memory -3: [00:24:56] done +3: [20:24:12] Testing Github940: property dictionaries leaking memory +3: [20:24:12] done 3: Testing RDValue 3: Testing RDAny 3: dict set int vect 3: dict get int vect -3: static boost any:0.000304 s +3: static boost any:0.000315 s 3: dynamic boost any:0.000914 s 3: static RDAny:0.000132 s -3: dynamic RDAny:0.000832 s -3: static RDValue:1e-06 s +3: dynamic RDAny:0.000834 s +3: static RDValue:0 s 3: dynamic RDValue:0.000161 s 3: deleted! -3: [00:24:56] ------------------------------------- -3: [00:24:56] Testing String Pickle Roundtrips. -3: [00:24:56] done -3: [00:24:56] ------------------------------------- -3: [00:24:56] Testing conversion of vect to string. -3: [00:24:56] done -3: [00:24:56] ------------------------------------- -3: [00:24:56] Testing returning const references. -3: [00:24:56] any cast -3: [00:24:56] done: 0.000727 300000 -3: [00:24:56] copy -3: [00:24:56] done: 0.000692 300000 -3: [00:24:56] ref -3: [00:24:56] done: 0.000775 300000 -3: [00:24:56] dict -3: [00:24:56] done: 0.00156 300000 -3: [00:24:56] ref with hasVal -3: [00:24:56] done: 0.001325 300000 -3: [00:24:56] done -3: [00:24:56] ------------------------------------- -3: [00:24:56] Testing dict update. -3: [00:24:56] done +3: [20:24:12] ------------------------------------- +3: [20:24:12] Testing String Pickle Roundtrips. +3: [20:24:12] done +3: [20:24:12] ------------------------------------- +3: [20:24:12] Testing conversion of vect to string. +3: [20:24:12] done +3: [20:24:12] ------------------------------------- +3: [20:24:12] Testing returning const references. +3: [20:24:12] any cast +3: [20:24:12] done: 0.000727 300000 +3: [20:24:12] copy +3: [20:24:12] done: 0.000692 300000 +3: [20:24:12] ref +3: [20:24:12] done: 0.000779 300000 +3: [20:24:12] dict +3: [20:24:12] done: 0.001567 300000 +3: [20:24:12] ref with hasVal +3: [20:24:12] done: 0.001494 300000 +3: [20:24:12] done +3: [20:24:12] ------------------------------------- +3: [20:24:12] Testing dict update. +3: [20:24:12] done 3: deleted! 3: deleted! 3: deleted! @@ -16085,48 +15749,48 @@ 4: == unsigned int 4: == bool 4: == std::string -5: [00:24:56] +5: [20:24:12] 5: ----------------------------------------- -5: [00:24:56] Finished: testPushAndPop() -5: [00:24:56] +5: [20:24:12] Finished: testPushAndPop() +5: [20:24:12] 5: ----------------------------------------- -5: [00:24:56] +5: [20:24:12] 5: ----------------------------------------- -6: Randomness seeded to: 227079761 +6: Randomness seeded to: 3952290050 6: =============================================================================== 6: All tests passed (32 assertions in 2 test cases) 6: -7: [00:24:56] should not be silent -7: [00:24:56] should not be silent -7: Randomness seeded to: 134992603 -7: [00:24:56] should not be silent -7: [00:24:56] should not be silent -7: [00:24:56] should not be silent -7: [00:24:56] should not be silent -7: [00:24:56] should not be silent -7: [00:24:56] should not be silent -7: [00:24:56] should not be silent -7: [00:24:56] should not be silent +7: [20:24:12] should not be silent +7: [20:24:12] should not be silent +7: Randomness seeded to: 2239296165 +7: [20:24:12] should not be silent +7: [20:24:12] should not be silent +7: [20:24:12] should not be silent +7: [20:24:12] should not be silent +7: [20:24:12] should not be silent +7: [20:24:12] should not be silent +7: [20:24:12] should not be silent +7: [20:24:12] should not be silent 7: =============================================================================== 7: All tests passed (26 assertions in 3 test cases) 7: -8: [00:24:56] pass -8: [00:24:56] v3 4 -8: [00:24:56] v4 5 -8: [00:24:56] SPARSE ----------------------------------- -8: [00:24:56] Set 10: 0 -8: [00:24:56] Set 11: 0 -8: [00:24:56] Set 14: 0 -8: [00:24:56] Set 10: 1 -8: [00:24:56] Get 14: 1 -8: [00:24:56] Num: 20 -8: [00:24:56] NumOn: 3 -8: [00:24:56] NumOff: 17 +8: [20:24:12] pass +8: [20:24:12] v3 4 +8: [20:24:12] v4 5 +8: [20:24:12] SPARSE ----------------------------------- +8: [20:24:12] Set 10: 0 +8: [20:24:12] Set 11: 0 +8: [20:24:12] Set 14: 0 +8: [20:24:12] Set 10: 1 +8: [20:24:12] Get 14: 1 +8: [20:24:12] Num: 20 +8: [20:24:12] NumOn: 3 +8: [20:24:12] NumOff: 17 8: 10, 11, 14, -8: [00:24:56] t2[19]: 0 -8: [00:24:56] t2[14]: 1 -8: [00:24:56] t2[19]: 0 -8: [00:24:56] t2[14]: 0 +8: [20:24:12] t2[19]: 0 +8: [20:24:12] t2[14]: 1 +8: [20:24:12] t2[19]: 0 +8: [20:24:12] t2[14]: 0 8: t1: 10, 11, 14, 8: t2: 10, 11, 15, 17, 8: t1|t2: 10, 11, 14, 15, 17, @@ -16134,20 +15798,20 @@ 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: [00:24:56] Explicit ---------------------------------- -8: [00:24:56] Set 10: 0 -8: [00:24:56] Set 11: 0 -8: [00:24:56] Set 14: 0 -8: [00:24:56] Set 10: 1 -8: [00:24:56] Get 14: 1 -8: [00:24:56] Num: 20 -8: [00:24:56] NumOn: 3 -8: [00:24:56] NumOff: 17 +8: [20:24:12] Explicit ---------------------------------- +8: [20:24:12] Set 10: 0 +8: [20:24:12] Set 11: 0 +8: [20:24:12] Set 14: 0 +8: [20:24:12] Set 10: 1 +8: [20:24:12] Get 14: 1 +8: [20:24:12] Num: 20 +8: [20:24:12] NumOn: 3 +8: [20:24:12] NumOff: 17 8: 10, 11, 14, -8: [00:24:56] t2[19]: 0 -8: [00:24:56] t2[14]: 1 -8: [00:24:56] t2[19]: 0 -8: [00:24:56] t2[14]: 0 +8: [20:24:12] t2[19]: 0 +8: [20:24:12] t2[14]: 1 +8: [20:24:12] t2[19]: 0 +8: [20:24:12] t2[14]: 0 8: t1: 10, 11, 14, 8: t2: 10, 11, 15, 17, 8: t1|t2: 10, 11, 14, 15, 17, @@ -16155,34 +15819,34 @@ 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: [00:24:56] Done -8: [00:24:56] Test DiscreteValue Vectors 1 ---------------------------- -8: [00:24:56] Expected failure: Value out of range -8: [00:24:56] Expected failure: Value out of range -8: [00:24:56] Expected failure: Value out of range -8: [00:24:56] Expected failure: Value out of range -8: [00:24:56] Expected failure: Value out of range -8: [00:24:56] Test DiscreteValue Vectors 2 ------------------------------ -8: [00:24:56] Test DiscreteValue Vectors 3 --------------------------- -8: [00:24:56] Test DiscreteValue Operations ----------------------------- -8: [00:24:56] Test DiscreteValue Operations 2 -------------------------- -8: [00:24:56] Test SparseIntVect ------------------------------------ -8: [00:24:56] Test SparseIntVect Serialization -------------------------- -8: [00:24:56] Test BitVect Serialization ------------------------------- -8: [00:24:56] Test BitVect to FPS ------------------------------- -8: [00:24:56] Test BitVect to binary string ------------------------------- -8: [00:24:56] Test Similarity Measures BitVect ------------------------------- -8: [00:24:56] Test Similarity Measures SparseBitVect ------------------------------- -8: [00:24:56] Test BitVect with all ones ------------------------------- -8: [00:24:56] Test Explicit BitVects: Concatenation Operation ------------------------------- -8: [00:24:56] Test bitmap operations ------------------------------- -8: [00:24:56] Test bitmaps as properties ------------------------------- -8: [00:24:56] Test #3944: SparseIntVect copy constructor and assignment operators not clearing existing data------------------------------- -8: [00:24:56] Test RealValue Vectors 1: Constructors and Accessing Values ------------------------------- -8: [00:24:56] Test RealValue Vectors 2: L1Norm ------------------------------- -8: [00:24:56] Test RealValue Vectors 3: Pickles ------------------------------- -8: [00:24:56] Test RealValue Vectors 4: Vector Operations ------------------------------- -11: Randomness seeded to: 3310960325 +8: [20:24:12] Done +8: [20:24:12] Test DiscreteValue Vectors 1 ---------------------------- +8: [20:24:12] Expected failure: Value out of range +8: [20:24:12] Expected failure: Value out of range +8: [20:24:12] Expected failure: Value out of range +8: [20:24:12] Expected failure: Value out of range +8: [20:24:12] Expected failure: Value out of range +8: [20:24:12] Test DiscreteValue Vectors 2 ------------------------------ +8: [20:24:12] Test DiscreteValue Vectors 3 --------------------------- +8: [20:24:12] Test DiscreteValue Operations ----------------------------- +8: [20:24:12] Test DiscreteValue Operations 2 -------------------------- +8: [20:24:12] Test SparseIntVect ------------------------------------ +8: [20:24:12] Test SparseIntVect Serialization -------------------------- +8: [20:24:12] Test BitVect Serialization ------------------------------- +8: [20:24:12] Test BitVect to FPS ------------------------------- +8: [20:24:12] Test BitVect to binary string ------------------------------- +8: [20:24:12] Test Similarity Measures BitVect ------------------------------- +8: [20:24:12] Test Similarity Measures SparseBitVect ------------------------------- +8: [20:24:12] Test BitVect with all ones ------------------------------- +8: [20:24:12] Test Explicit BitVects: Concatenation Operation ------------------------------- +8: [20:24:12] Test bitmap operations ------------------------------- +8: [20:24:12] Test bitmaps as properties ------------------------------- +8: [20:24:12] Test #3944: SparseIntVect copy constructor and assignment operators not clearing existing data------------------------------- +8: [20:24:12] Test RealValue Vectors 1: Constructors and Accessing Values ------------------------------- +8: [20:24:12] Test RealValue Vectors 2: L1Norm ------------------------------- +8: [20:24:12] Test RealValue Vectors 3: Pickles ------------------------------- +8: [20:24:12] Test RealValue Vectors 4: Vector Operations ------------------------------- +11: Randomness seeded to: 1115724838 11: =============================================================================== 11: All tests passed (3 assertions in 1 test case) 11: @@ -16194,8 +15858,8 @@ 17: testPointOps2D 17: **************************************** 17: test12D -17: ref1: 4.49077 0.241581 ref2: 1.23227 3.07734 -17: pt1: 0.49677 4.82358 pt2: 0.88942 0.327508 +17: ref1: 4.06577 2.30901 ref2: 0.532168 3.93563 +17: pt1: 1.4801 3.50083 pt2: 4.41968 3.09108 17: **************************************** 17: test23D 17: **************************************** @@ -16210,51 +15874,20 @@ 17: **************************************** 17: testFromQuaternion 17: **************************************** -18: *********************************************************** -18: Testing Grid -18: --------------------------------- -18: testUniformGrid1 -18: -18: --------------------------------- -18: testUniformGrid2 -18: -18: --------------------------------- -18: testUniformGridPickling -18: -18: --------------------------------- -18: testGridOps -18: -18: --------------------------------- -18: testUniformGridIndexing -18: -19: *********************************************************** -19: Testing RealValueGrid3D -19: --------------------------------- -19: test1UniformRealValueGrid3D -19: -19: --------------------------------- -19: test2UniformRealValueGrid3DPickling -19: -19: --------------------------------- -19: test3UniformRealValueGrid3DIndexing -19: -19: --------------------------------- -19: test4UniformRealValueGrid3DOps -19: -20: Randomness seeded to: 478799743 +20: Randomness seeded to: 3225440714 20: =============================================================================== 20: All tests passed (50 assertions in 5 test cases) 20: -22: [00:24:56] ----------------------------------------- -22: [00:24:56] Testing RDNumerics: vectors and matrices Code -22: [00:24:56] --------------------------------------- -22: [00:24:56] test1Vector -22: [00:24:56] --------------------------------------- -22: [00:24:56] test2Matrix -22: [00:24:56] --------------------------------------- -22: [00:24:56] test3SquareMatrix -22: [00:24:56] --------------------------------------- -22: [00:24:56] test4SymmMatrix +22: [20:24:12] ----------------------------------------- +22: [20:24:12] Testing RDNumerics: vectors and matrices Code +22: [20:24:12] --------------------------------------- +22: [20:24:12] test1Vector +22: [20:24:12] --------------------------------------- +22: [20:24:12] test2Matrix +22: [20:24:12] --------------------------------------- +22: [20:24:12] test3SquareMatrix +22: [20:24:12] --------------------------------------- +22: [20:24:12] test4SymmMatrix 24: ----------------------------------------- 24: Testing Alignment Code 24: --------------------------------------- @@ -16272,73 +15905,31 @@ 26: ------------------------------------- 26: Testing BFGS optimization. 26: done -27: Randomness seeded to: 1019036773 -27: =============================================================================== -27: All tests passed (20 assertions in 2 test cases) -27: -28: ------------------------------------- -28: Unit tests for force field basics. -28: done -28: ------------------------------------- -28: Unit tests for basics of UFF bond-stretch terms. -28: done -28: ------------------------------------- -28: Unit tests for UFF bond-stretch terms. -28: done -28: ------------------------------------- -28: Unit tests for basics of UFF angle terms. -28: done -28: ------------------------------------- -28: Unit tests for UFF angle-bend terms. -28: theta = 3.14159; theta0 = 3.14159 -28: theta = 2.094395, param1.theta0 = 2.094395 -28: done -28: ------------------------------------- -28: Test Simple UFF molecule optimizations. -28: done -28: ------------------------------------- -28: Unit tests for UFF nonbonded terms. -28: done -28: ------------------------------------- -28: Test UFF torsional terms. -28: done -28: ------------------------------------- -28: Test UFF Parameter objects -28: ------------------------------------- -28: Test Simple UFF molecule optimization, part 2. -28: done -28: ------------------------------------- -28: Test UFF Torsion Conflicts. -28: C 0.4783 -0.7477 -0.0753 -28: C -0.5465 -0.0176 0.3519 -28: C -0.5114 1.4472 0.0870 -28: H -1.5201 -0.4838 0.2485 -28: H 0.4696 1.8363 0.3367 -28: O -1.2618 1.9423 0.6934 -28: F -0.7163 1.6298 -0.9622 -28: done -28: ------------------------------------- -28: Unit tests for UFF distance constraint terms. -28: done -28: ------------------------------------- -28: Unit tests for all UFF constraint terms. - 1/236 Test #1: testCoordGen ........................... Passed 0.24 sec - 2/236 Test #3: testDict ............................... Passed 0.24 sec - 3/236 Test #4: testRDValue ............................ Passed 0.24 sec - 4/236 Test #6: dictTestsCatch ......................... Passed 0.23 sec - 5/236 Test #7: logTestsCatch .......................... Passed 0.23 sec - 6/236 Test #8: testDataStructs ........................ Passed 0.23 sec - 7/236 Test #9: testFPB ................................ Passed 0.23 sec - 8/236 Test #10: testMultiFPB ........................... Passed 0.23 sec - 9/236 Test #11: catchDataStructs ....................... Passed 0.23 sec - 10/236 Test #17: testTransforms ......................... Passed 0.22 sec - 11/236 Test #18: testGrid ............................... Passed 0.22 sec - 12/236 Test #19: testRealValueGrid ...................... Passed 0.22 sec - 13/236 Test #20: geometryTestsCatch ..................... Passed 0.22 sec - 14/236 Test #22: testMatrices ........................... Passed 0.09 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 + 1/236 Test #3: testDict ............................... Passed 0.07 sec + 2/236 Test #4: testRDValue ............................ Passed 0.07 sec + 3/236 Test #6: dictTestsCatch ......................... Passed 0.06 sec + 4/236 Test #7: logTestsCatch .......................... Passed 0.06 sec + 5/236 Test #8: testDataStructs ........................ Passed 0.06 sec + 6/236 Test #9: testFPB ................................ Passed 0.06 sec + 7/236 Test #10: testMultiFPB ........................... Passed 0.06 sec + 8/236 Test #11: catchDataStructs ....................... Passed 0.06 sec + 9/236 Test #17: testTransforms ......................... Passed 0.05 sec + 10/236 Test #20: geometryTestsCatch ..................... Passed 0.04 sec + 11/236 Test #22: testMatrices ........................... Passed 0.04 sec + 12/236 Test #24: testAlignment .......................... Passed 0.04 sec + 13/236 Test #26: testOptimizer .......................... Passed 0.03 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 @@ -16405,6 +15996,171 @@ 53: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/queryTestsCatch 53: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol 53: Test timeout computed to be: 1500 +19: *********************************************************** +19: Testing RealValueGrid3D +19: --------------------------------- +19: test1UniformRealValueGrid3D +19: +19: --------------------------------- +19: test2UniformRealValueGrid3DPickling +19: +19: --------------------------------- +19: test3UniformRealValueGrid3DIndexing +19: +19: --------------------------------- +19: test4UniformRealValueGrid3DOps +19: + 14/236 Test #19: testRealValueGrid ...................... Passed 0.08 sec +18: *********************************************************** +18: Testing Grid +18: --------------------------------- +18: testUniformGrid1 +18: +18: --------------------------------- +18: testUniformGrid2 +18: +18: --------------------------------- +18: testUniformGridPickling +18: +18: --------------------------------- +18: testGridOps +18: +18: --------------------------------- +18: testUniformGridIndexing +18: + 15/236 Test #18: testGrid ............................... Passed 0.08 sec +28: ------------------------------------- +28: Unit tests for force field basics. +28: done +28: ------------------------------------- +28: Unit tests for basics of UFF bond-stretch terms. +28: done +28: ------------------------------------- +28: Unit tests for UFF bond-stretch terms. +28: done +28: ------------------------------------- +28: Unit tests for basics of UFF angle terms. +28: done +28: ------------------------------------- +28: Unit tests for UFF angle-bend terms. +28: theta = 3.14159; theta0 = 3.14159 +28: theta = 2.094395, param1.theta0 = 2.094395 +28: done +28: ------------------------------------- +28: Test Simple UFF molecule optimizations. +28: done +28: ------------------------------------- +28: Unit tests for UFF nonbonded terms. +28: done +28: ------------------------------------- +28: Test UFF torsional terms. +28: done +28: ------------------------------------- +28: Test UFF Parameter objects +28: ------------------------------------- +28: Test Simple UFF molecule optimization, part 2. +28: done +28: ------------------------------------- +28: Test UFF Torsion Conflicts. +28: C 0.4783 -0.7477 -0.0753 +28: C -0.5465 -0.0176 0.3519 +28: C -0.5114 1.4472 0.0870 +28: H -1.5201 -0.4838 0.2485 +28: H 0.4696 1.8363 0.3367 +28: O -1.2618 1.9423 0.6934 +28: F -0.7163 1.6298 -0.9622 +28: done +28: ------------------------------------- +28: Unit tests for UFF distance constraint terms. +28: done +28: ------------------------------------- +28: Unit tests for all UFF constraint terms. +28: done +28: ------------------------------------- +28: Unit tests for copying UFF ForceFields. +28: done +28: ------------------------------------- +28: Unit test for UFF butane scan. +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: + 16/236 Test #31: testDistGeom ........................... Passed 0.07 sec +27: Randomness seeded to: 2603524442 +27: =============================================================================== +27: All tests passed (20 assertions in 2 test cases) +27: + 17/236 Test #27: ForceFieldsCatch ....................... Passed 0.07 sec +29: ------------------------------------- +29: Official MMFF validation suite. +33: +33: +33: +33: COPY + 18/236 Test #33: graphmolcpTest ......................... Passed 0.06 sec +34: [20:24:12] ---------------------- Test1 +34: [20:24:12] Done! +34: [20:24:12] ---------------------- Test2 +34: [20:24:12] Done! +34: [20:24:12] ---------------------- Test3 +34: [20:24:12] Done! +34: [20:24:12] ---------------------- Test4 +34: [20:24:12] Done! +34: [20:24:12] ---------------------- Test5 +34: [20:24:12] Done! +34: [20:24:12] +34: +34: **** +34: Pre-condition Violation +34: Can't expand empty query +34: Violation occurred on line 30 in file ./Code/GraphMol/QueryAtom.cpp +34: Failed Expression: dp_query +34: ---------- +34: Stacktrace: +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# 0x000055B02CF337EB in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolqueryTest +34: 4# 0x000055B02CF310AB in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolqueryTest +34: 5# 0x00007FD565233CA8 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# 0x000055B02CF31121 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolqueryTest +34: ---------- +34: **** +34: +34: [20:24:12] Done! +34: [20:24:12] ---------------------- Test issue 2892580 +34: [20:24:12] Done! +34: [20:24:12] ---------------------- Test github issue 53: query molecules not matching [R] +34: [20:24:12] Done! +34: [20:24:12] ---------------------- Test queries using qualifiers instead of == +34: [20:24:12] Done! +34: [20:24:12] ---------------------- Test Github issue 165: radicals not used in atom-atom matching +34: [20:24:12] Done! +34: [20:24:12] ---------------------- Test extra atom queries +34: [20:24:12] Done! +34: [20:24:12] ---------------------- Test extra bond queries +34: [20:24:12] Done! +34: [20:24:12] ---------------------- Test num heteroatom neighbor queries +34: [20:24:12] Done! +34: [20:24:12] ---------------------- Test atom type queries +34: [20:24:12] Done! +34: [20:24:12] ---------------------- Test Github #2471: dummy atom queries are flagged as complex +34: [20:24:12] Done! +34: [20:24:12] ---------------------- Testing hasBondTypeQuery() and hasComplexBondTypeQuery() +34: [20:24:12] Done! +37: [20:24:12] ------------------------------------- +37: [20:24:12] Testing String Pickle Roundtrips. +37: [20:24:12] done +37: [20:24:12] ------------------------------------- +37: [20:24:12] Testing reading existing pickle file (v2). test 54 Start 54: molbundleTestsCatch @@ -16435,115 +16191,1008 @@ 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 +40: [20:24:12] Testing the hanoi sort +40: [20:24:12] populating vectors +35: 1 1 2 +35: 1 1 1 +35: 2 1 0.75 +35: path: 2 +35: [20:24:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored +35: [20:24:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored +35: [20:24:12] Explicit valence for atom # 0 B, 5, is greater than permitted +35: [20:24:12] Explicit valence for atom # 1 C, 5, is greater than permitted +35: [20:24:12] Explicit valence for atom # 1 C, 5, is greater than permitted +35: [20:24:12] Explicit valence for atom # 1 C, 5, is greater than permitted +35: [20:24:12] Explicit valence for atom # 1 Si, 7, is greater than permitted +38: [20:24:12] done +36: -------------------------- +36: -------------------------- +36: C/C=C/C(C)Cl +36: [20:24:12] Conflicting single bond directions around double bond at index 2. +36: [20:24:12] BondStereo set to STEREONONE and single bond directions set to NONE. +36: [20:24:12] Conflicting single bond directions around double bond at index 4. +36: [20:24:12] BondStereo set to STEREONONE and single bond directions set to NONE. +36: [20:24:12] Conflicting single bond directions around double bond at index 15. +36: [20:24:12] BondStereo set to STEREONONE and single bond directions set to NONE. +36: [20:24:12] Conflicting single bond directions around double bond at index 2. +36: [20:24:12] BondStereo set to STEREONONE and single bond directions set to NONE. +36: [20:24:12] Conflicting single bond directions around double bond at index 1. +36: [20:24:12] BondStereo set to STEREONONE and single bond directions set to NONE. +36: -------------------------------------------------- +23: Randomness seeded to: 4082987616 +23: =============================================================================== +23: All tests passed (76 assertions in 3 test cases) +23: + 19/236 Test #23: testConrec ............................. Passed 0.10 sec + 20/236 Test #34: graphmolqueryTest ...................... Passed 0.08 sec + 21/236 Test #38: graphmoltestPicklerGlobalSetting ....... Passed 0.07 sec + 22/236 Test #39: graphmolIterTest ....................... Passed 0.07 sec + 23/236 Test #41: graphmolMemTest1 ....................... Passed 0.06 sec + 24/236 Test #43: molBundleTest .......................... Passed 0.05 sec + 25/236 Test #45: test-valgrind .......................... Passed 0.05 sec 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 -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... -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 0.13 sec -23: Randomness seeded to: 837336326 -23: =============================================================================== -23: All tests passed (76 assertions in 3 test cases) -23: - 19/236 Test #23: testConrec ............................. Passed 0.18 sec -33: -33: -33: -33: COPY - 20/236 Test #33: graphmolcpTest ......................... Passed 0.13 sec -16: ......... -16: ---------------------------------------------------------------------- -16: Ran 9 tests in 0.003s -16: -16: OK -34: [00:24:56] ---------------------- Test1 -34: [00:24:56] Done! -34: [00:24:56] ---------------------- Test2 -34: [00:24:56] Done! -34: [00:24:56] ---------------------- Test3 -34: [00:24:56] Done! -34: [00:24:56] ---------------------- Test4 -34: [00:24:56] Done! -34: [00:24:56] ---------------------- Test5 -34: [00:24:56] Done! -34: [00:24:56] -34: -34: **** -34: Pre-condition Violation -34: Can't expand empty query -34: Violation occurred on line 30 in file ./Code/GraphMol/QueryAtom.cpp -34: Failed Expression: dp_query -34: ---------- -34: Stacktrace: -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# 0x0000558626A787EB in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolqueryTest -34: 4# 0x0000558626A760AB in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolqueryTest -34: 5# 0x00007FACBDA33CA8 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# 0x0000558626A76121 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolqueryTest -34: ---------- -34: **** -34: -34: [00:24:56] Done! -34: [00:24:56] ---------------------- Test issue 2892580 -34: [00:24:56] Done! -34: [00:24:56] ---------------------- Test github issue 53: query molecules not matching [R] -34: [00:24:56] Done! -34: [00:24:56] ---------------------- Test queries using qualifiers instead of == -34: [00:24:56] Done! -34: [00:24:56] ---------------------- Test Github issue 165: radicals not used in atom-atom matching -34: [00:24:56] Done! -34: [00:24:56] ---------------------- Test extra atom queries -34: [00:24:56] Done! -34: [00:24:56] ---------------------- Test extra bond queries -34: [00:24:56] Done! -34: [00:24:56] ---------------------- Test num heteroatom neighbor queries -34: [00:24:56] Done! -34: [00:24:56] ---------------------- Test atom type queries -34: [00:24:56] Done! -34: [00:24:56] ---------------------- Test Github #2471: dummy atom queries are flagged as complex -34: [00:24:56] Done! -34: [00:24:56] ---------------------- Testing hasBondTypeQuery() and hasComplexBondTypeQuery() -34: [00:24:56] Done! - 21/236 Test #34: graphmolqueryTest ...................... Passed 0.13 sec -35: 1 1 2 -35: 1 1 1 -35: 2 1 0.75 -35: path: 2 -35: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored -35: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored -35: [00:24:56] Explicit valence for atom # 0 B, 5, is greater than permitted -35: [00:24:56] Explicit valence for atom # 1 C, 5, is greater than permitted -35: [00:24:56] Explicit valence for atom # 1 C, 5, is greater than permitted -35: [00:24:56] Explicit valence for atom # 1 C, 5, is greater than permitted -35: [00:24:56] 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 -37: [00:24:56] ------------------------------------- -37: [00:24:56] Testing String Pickle Roundtrips. -37: [00:24:56] done -37: [00:24:56] ------------------------------------- -37: [00:24:56] Testing reading existing pickle file (v2). -37: [00:24:56] done -37: [00:24:56] ------------------------------------- -37: [00:24:56] Testing combining molecules using pickles. +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 + 26/236 Test #36: graphmoltestChirality .................. Passed 0.10 sec +46: Randomness seeded to: 3872796996 +46: [20:24:12] WARNING: not removing hydrogen atom without neighbors +46: [20:24:12] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +46: [20:24:12] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +46: [20:24:12] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +46: [20:24:12] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +46: [20:24:12] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +46: [20:24:12] Explicit valence for atom # 1 N, 5, is greater than permitted +46: [20:24:12] Explicit valence for atom # 1 N, 6, is greater than permitted +46: [20:24:12] Explicit valence for atom # 1 N, 5, is greater than permitted +46: [20:24:12] Explicit valence for atom # 1 N, 5, is greater than permitted +46: [20:24:12] Explicit valence for atom # 2 O, 3, is greater than permitted +46: [20:24:12] Explicit valence for atom # 2 O, 3, is greater than permitted +46: [20:24:12] non-ring atom 2 marked aromatic +46: [20:24:12] non-ring atom 2 marked aromatic +46: [20:24:12] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +46: [20:24:12] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +46: [20:24:12] Can't kekulize mol. Unkekulized atoms: 1 2 3 +46: [20:24:12] Can't kekulize mol. Unkekulized atoms: 1 2 3 +46: [20:24:12] Can't kekulize mol. Unkekulized atoms: 0 1 2 +46: [20:24:12] Can't kekulize mol. Unkekulized atoms: 0 1 2 +46: [20:24:12] Explicit valence for atom # 1 O, 3, is greater than permitted +46: [20:24:12] Explicit valence for atom # 4 F, 2, is greater than permitted +46: [20:24:12] Can't kekulize mol. Unkekulized atoms: 6 7 8 +46: [20:24:12] Explicit valence for atom # 1 C, 5, is greater than permitted +46: [20:24:12] WARNING: not removing hydrogen atom with dummy atom neighbors +46: [20:24:12] WARNING: not removing hydrogen atom with dummy atom neighbors +46: [20:24:12] WARNING: not removing hydrogen atom with wedged bond +46: [20:24:12] WARNING: not removing hydrogen atom without neighbors +46: [20:24:12] WARNING: not removing hydrogen atom without neighbors +46: [20:24:12] WARNING: not removing hydrogen atom without neighbors +46: [20:24:12] WARNING: not removing hydrogen atom without neighbors +46: [20:24:12] Unreasonable formal charge on atom # 0. +46: [20:24:12] +46: +46: **** +46: Pre-condition Violation +46: no atom +46: Violation occurred on line 181 in file ./Code/GraphMol/ROMol.cpp +46: Failed Expression: at +46: ---------- +46: Stacktrace: +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# 0x000056069CEBC668 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x000056069CF09938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x000056069CF0A458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x000056069CF0A8D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x000056069CEDBF43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x000056069CEDC2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x000056069CE56DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007F30DC433CA8 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# 0x000056069CE56E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: ---------- +46: **** +46: +46: [20:24:12] +46: +46: **** +46: Pre-condition Violation +46: no owner +46: Violation occurred on line 153 in file ./Code/GraphMol/Atom.h +46: Failed Expression: dp_mol +46: ---------- +46: Stacktrace: +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# 0x000056069CEBC6F2 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x000056069CF09938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x000056069CF0A458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x000056069CF0A8D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x000056069CEDBF43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x000056069CEDC2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x000056069CE56DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007F30DC433CA8 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# 0x000056069CE56E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: ---------- +46: **** +46: +46: [20:24:12] +46: +46: **** +46: Pre-condition Violation +46: atom not associated with this molecule +46: Violation occurred on line 182 in file ./Code/GraphMol/ROMol.cpp +46: Failed Expression: &at->getOwningMol() == this +46: ---------- +46: Stacktrace: +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# 0x000056069CEBC785 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x000056069CF09938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x000056069CF0A458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x000056069CF0A8D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x000056069CEDBF43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x000056069CEDC2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x000056069CE56DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007F30DC433CA8 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# 0x000056069CE56E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: ---------- +46: **** +46: +46: [20:24:12] +46: +46: **** +46: Pre-condition Violation +46: no atom +46: Violation occurred on line 364 in file ./Code/GraphMol/ROMol.cpp +46: Failed Expression: at +46: ---------- +46: Stacktrace: +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# 0x000056069CEBC870 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x000056069CF09938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x000056069CF0A458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x000056069CF0A8D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x000056069CEDBF43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x000056069CEDC2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x000056069CE56DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007F30DC433CA8 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# 0x000056069CE56E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: ---------- +46: **** +46: +46: [20:24:12] +46: +46: **** +46: Pre-condition Violation +46: no owner +46: Violation occurred on line 153 in file ./Code/GraphMol/Atom.h +46: Failed Expression: dp_mol +46: ---------- +46: Stacktrace: +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# 0x000056069CEBC901 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x000056069CF09938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x000056069CF0A458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x000056069CF0A8D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x000056069CEDBF43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x000056069CEDC2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x000056069CE56DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007F30DC433CA8 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# 0x000056069CE56E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: ---------- +46: **** +46: +46: [20:24:12] +46: +46: **** +46: Pre-condition Violation +46: atom not associated with this molecule +46: Violation occurred on line 365 in file ./Code/GraphMol/ROMol.cpp +46: Failed Expression: &at->getOwningMol() == this +46: ---------- +46: Stacktrace: +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# 0x000056069CEBC99D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x000056069CF09938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x000056069CF0A458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x000056069CF0A8D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x000056069CEDBF43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x000056069CEDC2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x000056069CE56DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007F30DC433CA8 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# 0x000056069CE56E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: ---------- +46: **** +46: +46: [20:24:12] +46: +46: **** +46: Pre-condition Violation +46: no atom +46: Violation occurred on line 371 in file ./Code/GraphMol/ROMol.cpp +46: Failed Expression: at +46: ---------- +46: Stacktrace: +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# 0x000056069CEBD2B9 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x000056069CF09938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x000056069CF0A458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x000056069CF0A8D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x000056069CEDBF43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x000056069CEDC2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x000056069CE56DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007F30DC433CA8 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# 0x000056069CE56E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: ---------- +46: **** +46: +46: [20:24:12] +46: +46: **** +46: Pre-condition Violation +46: no owner +46: Violation occurred on line 153 in file ./Code/GraphMol/Atom.h +46: Failed Expression: dp_mol +46: ---------- +46: Stacktrace: +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# 0x000056069CEBCB08 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x000056069CF09938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x000056069CF0A458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x000056069CF0A8D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x000056069CEDBF43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x000056069CEDC2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x000056069CE56DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007F30DC433CA8 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# 0x000056069CE56E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: ---------- +46: **** +46: +46: [20:24:12] +46: +46: **** +46: Pre-condition Violation +46: atom not associated with this molecule +46: Violation occurred on line 372 in file ./Code/GraphMol/ROMol.cpp +46: Failed Expression: &at->getOwningMol() == this +46: ---------- +46: Stacktrace: +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# 0x000056069CEBCBA2 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x000056069CF09938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x000056069CF0A458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x000056069CF0A8D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x000056069CEDBF43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x000056069CEDC2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x000056069CE56DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007F30DC433CA8 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# 0x000056069CE56E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: ---------- +46: **** +46: +46: [20:24:12] +46: +46: **** +46: Pre-condition Violation +46: null atom passed in +46: Violation occurred on line 386 in file ./Code/GraphMol/ROMol.cpp +46: Failed Expression: atom_pin +46: ---------- +46: Stacktrace: +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# 0x000056069CEBD291 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x000056069CF09938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x000056069CF0A458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x000056069CF0A8D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x000056069CEDBF43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x000056069CEDC2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x000056069CE56DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007F30DC433CA8 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# 0x000056069CE56E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: ---------- +46: **** +46: +46: [20:24:12] +46: +46: **** +46: Pre-condition Violation +46: cannot take ownership of an atom which already has an owner +46: Violation occurred on line 387 in file ./Code/GraphMol/ROMol.cpp +46: Failed Expression: !takeOwnership || !atom_pin->hasOwningMol() || &atom_pin->getOwningMol() == this +46: ---------- +46: Stacktrace: +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# 0x000056069CEBCEB8 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x000056069CF09938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x000056069CF0A458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x000056069CF0A8D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x000056069CEDBF43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x000056069CEDC2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x000056069CE56DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007F30DC433CA8 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# 0x000056069CE56E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: ---------- +46: **** +46: +46: [20:24:12] +46: +46: **** +46: Pre-condition Violation +46: cannot take ownership of an bond which already has an owner +46: Violation occurred on line 412 in file ./Code/GraphMol/ROMol.cpp +46: Failed Expression: !takeOwnership || !bond_pin->hasOwningMol() || &bond_pin->getOwningMol() == this +46: ---------- +46: Stacktrace: +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# 0x000056069CEBD26D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x000056069CF09938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x000056069CF0A458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x000056069CF0A8D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x000056069CEDBF43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x000056069CEDC2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x000056069CE56DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007F30DC433CA8 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# 0x000056069CE56E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: ---------- +46: **** +46: +46: [20:24:12] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +46: [20:24:12] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +46: [20:24:12] WARNING: not removing hydrogen atom without neighbors +46: [20:24:12] Explicit valence for atom # 1 F greater than permitted +46: [20:24:12] +46: +46: **** +46: Pre-condition Violation +46: plain atoms have no Query +46: Violation occurred on line 697 in file ./Code/GraphMol/Atom.cpp +46: Failed Expression: 0 +46: ---------- +46: Stacktrace: +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# 0x000056069CE6414B in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x000056069CF09938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x000056069CF0A458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x000056069CF0A8D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x000056069CEDBF43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x000056069CEDC2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x000056069CE56DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007F30DC433CA8 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# 0x000056069CE56E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: ---------- +46: **** +46: +46: [20:24:12] +46: +46: **** +46: Pre-condition Violation +46: plain atoms have no Query +46: Violation occurred on line 702 in file ./Code/GraphMol/Atom.cpp +46: Failed Expression: 0 +46: ---------- +46: Stacktrace: +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# 0x000056069CE641E0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x000056069CF09938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x000056069CF0A458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x000056069CF0A8D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x000056069CEDBF43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x000056069CEDC2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x000056069CE56DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007F30DC433CA8 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# 0x000056069CE56E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: ---------- +46: **** +46: +46: [20:24:12] +46: +46: **** +46: Pre-condition Violation +46: plain bonds have no Query +46: Violation occurred on line 207 in file ./Code/GraphMol/Bond.cpp +46: Failed Expression: 0 +46: ---------- +46: Stacktrace: +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# 0x000056069CE63E70 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x000056069CF09938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x000056069CF0A458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x000056069CF0A8D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x000056069CEDBF43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x000056069CEDC2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x000056069CE56DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007F30DC433CA8 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# 0x000056069CE56E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: ---------- +46: **** +46: +46: [20:24:12] +46: +46: **** +46: Pre-condition Violation +46: plain bonds have no query +46: Violation occurred on line 228 in file ./Code/GraphMol/Bond.cpp +46: Failed Expression: 0 +46: ---------- +46: Stacktrace: +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# 0x000056069CE63F05 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x000056069CF09938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x000056069CF0A458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x000056069CF0A8D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x000056069CEDBF43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x000056069CEDC2AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x000056069CE56DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007F30DC433CA8 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# 0x000056069CE56E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: ---------- +46: **** +46: +46: [20:24:12] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +46: [20:24:12] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +46: [20:24:12] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +46: [20:24:12] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +46: [20:24:12] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +46: [20:24:12] Unusual charge on atom 0 number of radical electrons set to zero +46: [20:24:12] Unusual charge on atom 0 number of radical electrons set to zero +46: [20:24:12] Unusual charge on atom 0 number of radical electrons set to zero +46: [20:24:12] non-ring atom 0 marked aromatic +46: [20:24:12] non-ring atom 0 marked aromatic +46: [20:24:12] Explicit valence for atom # 1 C, 5, is greater than permitted +46: [20:24:12] Explicit valence for atom # 9 C, 5, is greater than permitted +46: [20:24:12] Explicit valence for atom # 3 N, 4, is greater than permitted +46: [20:24:12] Explicit valence for atom # 15 C, 5, is greater than permitted +46: [20:24:12] Explicit valence for atom # 11 C, 5, is greater than permitted +46: [20:24:12] Explicit valence for atom # 9 C, 5, is greater than permitted +46: [20:24:12] Explicit valence for atom # 9 C, 5, is greater than permitted +46: [20:24:12] Explicit valence for atom # 9 C, 6, is greater than permitted +46: [20:24:12] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +46: [20:24:12] Can't kekulize mol. Unkekulized atoms: 7 +46: [20:24:12] Can't kekulize mol. Unkekulized atoms: 3 +46: [20:24:12] Can't kekulize mol. Unkekulized atoms: 3 7 +46: [20:24:12] Can't kekulize mol. Unkekulized atoms: 3 7 + 27/236 Test #44: testSGroup ............................. Passed 0.08 sec +48: Randomness seeded to: 1311481137 +48: =============================================================================== +48: All tests passed (136 assertions in 8 test cases) +48: + 28/236 Test #48: graphmolSGroupCatch .................... Passed 0.07 sec +52: Randomness seeded to: 2274211972 +52: =============================================================================== +52: All tests passed (14 assertions in 4 test cases) +52: + 29/236 Test #52: moliteratorTestsCatch .................. Passed 0.06 sec +53: Randomness seeded to: 3050446949 +53: =============================================================================== +53: All tests passed (10 assertions in 1 test case) +53: + 30/236 Test #53: queryTestsCatch ........................ Passed 0.06 sec +test 66 + Start 66: depictorCatch + +66: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/depictorCatch +66: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor +66: Test timeout computed to be: 1500 +test 67 + Start 67: pyDepictor + +67: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Depictor/Wrap/testDepictor.py" +67: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/Wrap +67: Test timeout computed to be: 1500 +test 68 + Start 68: testMrvToMol + +68: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +68: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse +68: Test timeout computed to be: 1500 +test 69 + Start 69: fileParsersTest1 + +69: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +69: Test timeout computed to be: 1500 +test 70 + Start 70: testAtropisomers + +70: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testAtropisomers +70: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +70: Test timeout computed to be: 1500 +46: [20:24:12] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +46: [20:24:12] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +54: Randomness seeded to: 3710342645 +54: =============================================================================== +54: All tests passed (6 assertions in 1 test case) +54: +50: Randomness seeded to: 1666676573 +50: [20:24:12] unable to set wavy bonds for double bonds: 3 +50: [20:24:12] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +50: [20:24:12] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +50: [20:24:12] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. +50: [20:24:12] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. +50: [20:24:12] Warning: ambiguous stereochemistry - overlapping neighbors - at atom 2 ignored +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: +56: Randomness seeded to: 799517134 +56: =============================================================================== +56: All tests passed (7 assertions in 2 test cases) +56: +47: Randomness seeded to: 2496691468 +47: =============================================================================== +47: All tests passed (62 assertions in 6 test cases) +47: +49: Randomness seeded to: 4249630905 +49: =============================================================================== +49: All tests passed (292 assertions in 12 test cases) +49: +55: Randomness seeded to: 1427141213 +55: =============================================================================== +55: All tests passed (45 assertions in 4 test cases) +55: +57: Randomness seeded to: 2664079400 +57: =============================================================================== +57: All tests passed (230 assertions in 7 test cases) +57: +58: [20:24:12] WARNING: not removing hydrogen atom without neighbors +58: [20:24:12] WARNING: not removing hydrogen atom without neighbors +58: [20:24:12] WARNING: not removing hydrogen atom without neighbors +58: [20:24:12] WARNING: not removing hydrogen atom without neighbors +58: [20:24:12] WARNING: not removing hydrogen atom without neighbors +58: [20:24:12] WARNING: not removing hydrogen atom without neighbors +58: [20:24:12] WARNING: not removing hydrogen atom without neighbors +58: [20:24:12] WARNING: not removing hydrogen atom without neighbors +58: [20:24:12] WARNING: not removing hydrogen atom without neighbors +58: [20:24:12] WARNING: not removing hydrogen atom without neighbors +58: [20:24:12] WARNING: not removing hydrogen atom without neighbors +58: [20:24:12] Invalid chiral specification on atom 0 +58: [20:24:12] Invalid chiral specification on atom 0 +58: [20:24:12] Invalid chiral specification on atom 0 +58: [20:24:12] Invalid chiral specification on atom 0 +58: [20:24:12] Invalid chiral specification on atom 0 +58: [20:24:12] SMILES Parse Error: unclosed ring for input: 'C1.C11.C' +58: [20:24:12] SMILES Parse Error: unclosed ring for input: 'C1C.CC11CCC' +37: [20:24:12] done +37: [20:24:12] ------------------------------------- +37: [20:24:12] 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 @@ -16560,37 +17209,37 @@ 37: 4 4->5 order: 1 37: 5 5->6 order: 1 37: 6 6->3 order: 1 -37: [00:24:56] done -37: [00:24:56] ------------------------------------- -37: [00:24:56] Testing Issue164: Roundtrip Pickle Failure. -37: [00:24:56] done -37: [00:24:56] ------------------------------------- -37: [00:24:56] Testing Issue219: Pickle Failure with Conformations. -37: [00:24:56] done -37: [00:24:56] ------------------------------------- -37: [00:24:56] Testing Issue220: Pickle problems with bond stereochemistry. -37: [00:24:56] done -37: [00:24:56] ------------------------------------- -37: [00:24:56] Testing query serialization. -37: [00:24:56] C=[$(C=O)] -37: [00:24:56] S(=O)(=O)-[C&H2][F,Br,I,Cl] S(=O)(=O)-[C&H2][F,Br,I,Cl] -37: [00:24:56] done -37: [00:24:56] ------------------------------------- -37: [00:24:56] Testing radical handling in pickles. -37: [00:24:56] done -37: [00:24:56] done -37: [00:24:56] ------------------------------------- -37: [00:24:56] Testing sf.net issue 2788233. -37: [00:24:56] done -37: [00:24:56] ------------------------------------- -37: [00:24:56] Testing sf.net issue 3202580. +37: [20:24:12] done +37: [20:24:12] ------------------------------------- +37: [20:24:12] Testing Issue164: Roundtrip Pickle Failure. +37: [20:24:12] done +37: [20:24:12] ------------------------------------- +37: [20:24:12] Testing Issue219: Pickle Failure with Conformations. +37: [20:24:12] done +37: [20:24:12] ------------------------------------- +37: [20:24:12] Testing Issue220: Pickle problems with bond stereochemistry. +37: [20:24:12] done +37: [20:24:12] ------------------------------------- +37: [20:24:12] Testing query serialization. +37: [20:24:12] C=[$(C=O)] +37: [20:24:12] S(=O)(=O)-[C&H2][F,Br,I,Cl] S(=O)(=O)-[C&H2][F,Br,I,Cl] +37: [20:24:12] done +37: [20:24:12] ------------------------------------- +37: [20:24:12] Testing radical handling in pickles. +37: [20:24:12] done +37: [20:24:12] done +37: [20:24:12] ------------------------------------- +37: [20:24:12] Testing sf.net issue 2788233. +37: [20:24:12] done +37: [20:24:12] ------------------------------------- +37: [20:24:12] Testing sf.net issue 3202580. 37: mass! 13.0034 -37: [00:24:56] done -37: [00:24:56] ------------------------------------- -37: [00:24:56] Testing sf.net issue 3316407. -37: [00:24:56] done -37: [00:24:56] ------------------------------------- -37: [00:24:56] Testing sf.net issue 3496759. +37: [20:24:12] done +37: [20:24:12] ------------------------------------- +37: [20:24:12] Testing sf.net issue 3316407. +37: [20:24:12] done +37: [20:24:12] ------------------------------------- +37: [20:24:12] Testing sf.net issue 3496759. 37: smi match: *C *C 37: smi match: **=* **=* 37: smi match: [N-]=[N+]=NC=O [N-]=[N+]=NC=O @@ -16618,55 +17267,6 @@ 37: smi match: O=CON(C=O)C=O O=CON(C=O)C=O 37: smi match: N#CC[OH] N#CC[OH] 37: smi match: N#CC=O N#CC=O -38: [00:24:56] done - 22/236 Test #38: graphmoltestPicklerGlobalSetting ....... Passed 0.12 sec - 23/236 Test #39: graphmolIterTest ....................... Passed 0.12 sec -40: [00:24:56] Testing the hanoi sort -40: [00:24:56] populating vectors - 24/236 Test #41: graphmolMemTest1 ....................... Passed 0.11 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 -test 66 - Start 66: depictorCatch - -66: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/depictorCatch -66: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor -66: Test timeout computed to be: 1500 - 25/236 Test #16: pyFPB .................................. Passed 0.38 sec 37: smi match: N#CS(=O)=O N#CS(=O)=O 37: smi match: CCOP(=O)(C#N)OCC CCOP(=O)(C#N)OCC 37: smi match: N#CN=N N#CN=N @@ -16820,6 +17420,104 @@ 37: smi match: O=N=O O=N=O 37: smi match: O=NO O=NO 37: smi match: ONO ONO +35: smi: Cc1ccc(S(=O)(=O)/N=C2\CC(=N\C(C)(C)C)/C2=N\C(C)(C)C)cc1 +35: [20:24:12] non-ring atom 0 marked aromatic +35: [20:24:12] non-ring atom 0 marked aromatic +35: [20:24:12] Conflicting single bond directions around double bond at index 17. +35: [20:24:12] BondStereo set to STEREONONE and single bond directions set to NONE. +35: starting ring finding +35: done +35: starting ring finding +35: done +35: starting ring finding +35: done +35: C/C=N/c1ccc(cc1)c1cc2cc(c1)c1ccc(cc1)N=Cc1ccc(cc1)c1cc(cc(c1)c1ccc(cc1)C)c1ccc(cc1)C=Nc1ccc(cc1)c1cc(cc(c1)c1ccc(cc1)/N=C/C)c1ccc(cc1)N=Cc1ccc(cc1)c1cc(c3ccc(C=Nc4ccc(c5cc6c7ccc(N=Cc8ccc(c9cc(c%10ccc(C=Nc%11ccc2cc%11)cc%10)cc(c9)c2ccc(cc2)C=Nc2ccc(cc2)c2cc(cc(c2)c2ccc(cc2)N=Cc2ccc(cc2)c2cc(cc(c2)c2ccc(cc2)C)c2ccc(cc2)C=Nc2ccc(cc2)c2cc(c9ccc(N=Cc%10ccc(c%11cc(c%12ccc(C=Nc%13ccc(c(c6)c5)cc%13)cc%12)cc(c%11)c5ccc(cc5)C)cc%10)cc9)cc(c2)c2ccc(cc2)/N=C/C)c2ccc(cc2)/N=C/C)cc8)cc7)cc4)cc3)cc(c1)c1ccc(cc1)C +35: starting sanitization +59: [20:24:12] SMILES Parse Error: Failed parsing SMILES 'CO' for input: 'CO' +59: [20:24:12] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' +59: [20:24:12] SMILES Parse Error: syntax error while parsing: - +59: [20:24:12] SMILES Parse Error: check for mistakes around position 1: +59: [20:24:12] - +59: [20:24:12] ^ +59: [20:24:12] SMILES Parse Error: Failed parsing SMILES '-' for input: '-' +59: [20:24:12] SMILES Parse Error: Failed parsing SMILES '[Bg]' for input: '[Bg]' +59: [20:24:12] SMILES Parse Error: Failed parsing SMILES 'C' for input: 'C' +59: [20:24:12] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' +59: [20:24:12] SMILES Parse Error: Failed parsing SMILES '*' for input: '*' +59: [20:24:12] SMARTS Parse Error: Failed parsing SMARTS 'CO' for input: 'CO' +59: [20:24:12] SMARTS Parse Error: Failed parsing SMARTS 'C-O' for input: 'C-O' +59: [20:24:12] SMARTS Parse Error: Failed parsing SMARTS '-' for input: '-' +59: [20:24:12] SMARTS Parse Error: Failed parsing SMARTS '[Bg]' for input: '[Bg]' +59: [20:24:12] SMARTS Parse Error: Failed parsing SMARTS 'C' for input: 'C' +59: [20:24:12] SMARTS Parse Error: Failed parsing SMARTS '-O' for input: '-O' +59: [20:24:12] SMARTS Parse Error: Failed parsing SMARTS '*' for input: '*' + 31/236 Test #47: graphmolOrganometallicsCatch ........... Passed 0.13 sec + 32/236 Test #49: graphmolAdjustQueryCatch ............... Passed 0.12 sec + 33/236 Test #54: molbundleTestsCatch .................... Passed 0.10 sec + 34/236 Test #55: pickleTestsCatch ....................... Passed 0.10 sec + 35/236 Test #56: tableTestsCatch ........................ Passed 0.10 sec + 36/236 Test #57: molopsTestsCatch ....................... Passed 0.09 sec + 37/236 Test #59: smiTest2 ............................... Passed 0.08 sec +test 71 + Start 71: testSquiggleDoubleBonds + +71: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testSquiggleDoubleBonds +71: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +71: Test timeout computed to be: 1500 +test 72 + Start 72: testMolSupplier + +72: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier +72: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +72: Test timeout computed to be: 1500 +test 73 + Start 73: testGeneralFileReader + +73: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testGeneralFileReader +73: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +73: Test timeout computed to be: 1500 +test 74 + Start 74: testMultithreadedMolSupplier + +74: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMultithreadedMolSupplier +74: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +74: Test timeout computed to be: 1500 +test 75 + Start 75: testMolWriter + +75: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolWriter +75: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +75: Test timeout computed to be: 1500 +test 76 + Start 76: testTplParser + +76: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testTplParser +76: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +76: Test timeout computed to be: 1500 +test 77 + Start 77: testMol2ToMol + +77: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMol2ToMol +77: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +77: Test timeout computed to be: 1500 +46: [20:24:12] Explicit valence for atom # 1 O, 3, is greater than permitted +46: [20:24:12] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +46: [20:24:12] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +46: [20:24:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +46: [20:24:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +46: [20:24:12] Invalid value for molAttachPoint: 4 on atom 1. Not expanding this atttachment point. +46: [20:24:12] Invalid value for _fromAttachPoint: -1 on atom 0. Not collapsing this atom +46: [20:24:12] Invalid value for _fromAttachPoint: 4 on atom 0. Not collapsing this atom +46: [20:24:12] non-ring atom 0 marked aromatic +46: [20:24:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +46: [20:24:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +46: [20:24:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +46: [20:24:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +50: =============================================================================== +50: All tests passed (2295 assertions in 80 test cases) +50: + 38/236 Test #50: chiralityTestsCatch .................... Passed 0.14 sec + 39/236 Test #1: testCoordGen ........................... Passed 0.24 sec 37: smi match: C1SCS1 C1SCS1 37: smi match: N=C=S N=C=S 37: smi match: N=C=N N=C=N @@ -16909,6 +17607,143 @@ 37: smi match: O=COC=O O=COC=O 37: smi match: N=C=O N=C=O 37: smi match: N=C=S N=C=S +29: +29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_dative.sdf... +64: Randomness seeded to: 2349631545 +64: =============================================================================== +64: All tests passed (14 assertions in 2 test cases) +64: + 40/236 Test #64: v2smiTestCatch ......................... Passed 0.10 sec +63: Randomness seeded to: 2656030782 +63: [20:24:12] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +63: [20:24:12] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +63: [20:24:12] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +63: [20:24:12] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +63: [20:24:12] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +63: [20:24:12] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +63: [20:24:12] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +63: [20:24:12] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +63: [20:24:12] ignoring non-tetrahedral stereo specification since setAllowNontetrahedralChirality() is false. +63: =============================================================================== +63: All tests passed (308 assertions in 9 test cases) +63: +62: Randomness seeded to: 3180944258 +62: [20:24:12] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +62: [20:24:12] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +62: [20:24:12] SMARTS Parse Error: unclosed ring for input: 'c1ccccc' +62: [20:24:12] SMARTS Parse Error: unclosed ring for input: 'C1C' +62: [20:24:12] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +62: [20:24:12] SMARTS Parse Error: syntax error while parsing: C)foo +62: [20:24:12] SMARTS Parse Error: Failed parsing SMARTS 'C)foo' for input: 'C)foo' +62: [20:24:12] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| +62: [20:24:12] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$|' for input: 'CCC |$foo;;bar$|' +62: [20:24:12] unrecognized CXSMILES CONNECT value: 'EU'. Assuming 'eu' +13: ...... +13: ---------------------------------------------------------------------- +13: Ran 6 tests in 0.003s +13: +13: OK +14: ...... +14: ---------------------------------------------------------------------- +14: Ran 6 tests in 0.002s +14: +14: OK + 41/236 Test #14: pyRealValueVect ........................ Passed 0.23 sec +15: ......... +15: ---------------------------------------------------------------------- +15: Ran 9 tests in 0.009s +15: +15: OK +68: Using new chirality perception +68: Test +68: +68: rxnStereoMarkedCrossed.mrv +68: +68: Test +68: +68: 145323811.mol +68: +68: [20:24:12] 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: [20:24:12] For a MultipleSgroup expansion, the matching orphaned bond was not found +68: The multiple sgroup will be ignored +70: [20:24:12] ---- Running with POSIX locale ----- +70: [20:24:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [20:24:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [20:24:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [20:24:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [20:24:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [20:24:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [20:24:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [20:24:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [20:24:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [20:24:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [20:24:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [20:24:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +test 78 + Start 78: testSequence + +78: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testSequence +78: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +78: Test timeout computed to be: 1500 +test 79 + Start 79: testExtendedStereoParsing + +79: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testExtendedStereoParsing +79: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +79: Test timeout computed to be: 1500 +test 80 + Start 80: fileParsersCatchTest + +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 +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 +46: [20:24:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +46: [20:24:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +46: [20:24:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +46: [20:24:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +46: [20:24:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +46: [20:24:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +46: [20:24:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +46: [20:24:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +46: [20:24:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 37: smi match: O~O O~O 37: smi match: N~[SiH4] N~[SiH4] 37: smi match: *P *P @@ -17006,6 +17841,109 @@ 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 + 42/236 Test #63: nontetrahedralCatch .................... Passed 0.12 sec + 43/236 Test #13: pyDiscreteValueVect .................... Passed 0.25 sec + 44/236 Test #15: pySparseIntVect ........................ Passed 0.25 sec +2: .... +2: ---------------------------------------------------------------------- +2: Ran 4 tests in 0.024s +2: +2: OK +35: done +35: starting sanitization +35: done +35: starting ring finding +35: done +35: starting ring finding +35: done +35: smiles: CC[C@]1(C(=O)c([nH])n)CC[C@](C)(O)CC1 +35: [20:24:12] WARNING: not removing hydrogen atom with dummy atom neighbors +35: ------------------------------- +35: [20:24:12] Explicit valence for atom # 0 N, 4, is greater than permitted +35: [20:24:12] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +35: [20:24:12] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +35: [20:24:12] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +35: [20:24:12] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +35: [20:24:12] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +35: [20:24:12] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +35: [20:24:12] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +35: [20:24:12] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +35: +35: [20:24:12] WARNING: not removing hydrogen atom with dummy atom neighbors +69: *************************************** +69: *************************************** +69: [20:24:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [20:24:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [20:24:12] bond with order 0 found on line 7. This is not part of the MDL specification. +69: [20:24:12] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) +69: [20:24:12] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) +69: [20:24:12] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +32: ...... +32: ---------------------------------------------------------------------- +32: Ran 6 tests in 0.001s +32: +32: OK +25: ..... +25: ---------------------------------------------------------------------- +25: Ran 5 tests in 0.002s +25: +25: OK +25: Testing Alignment Wrapper code: +16: ......... +16: ---------------------------------------------------------------------- +16: Ran 9 tests in 0.005s +16: +16: OK +71: Randomness seeded to: 2318345076 +71: =============================================================================== +71: All tests passed (15 assertions in 3 test cases) +71: + 45/236 Test #71: testSquiggleDoubleBonds ................ Passed 0.05 sec +72: [20:24:12] +72: ----------------------------------------- +73: [20:24:12] +73: ----------------------------------------- +73: [20:24:12] Finished: testDetermineFormat() +73: [20:24:12] ----------------------------------------- +73: +73: [20:24:12] +73: ----------------------------------------- +73: [20:24:12] Finished: testSdf() +73: [20:24:12] ----------------------------------------- +73: +73: [20:24:12] +73: ----------------------------------------- +73: [20:24:12] Finished: testSmi() +73: [20:24:12] ----------------------------------------- +73: +73: [20:24:12] +73: ----------------------------------------- +74: [20:24:12] +74: ----------------------------------------- +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 37: smi match: SS SS 37: smi match: * * 37: smi match: *=* *=* @@ -17066,930 +18004,64 @@ 37: smi match: * * 37: smi match: ***** ***** 37: smi match: NC(N)=O NC(N)=O -37: [00:24:56] done -37: [00:24:56] ------------------------------------- -37: [00:24:56] Testing sf.net issue 280. -37: [00:24:56] done -37: [00:24:56] ------------------------------------- -37: [00:24:56] Testing sf.net issue 285. -37: [00:24:56] done -37: [00:24:56] done -37: [00:24:56] done -37: [00:24:56] done -37: [00:24:56] done -37: [00:24:56] done -37: [00:24:56] done -37: [00:24:56] ------------------------------------- -37: [00:24:56] Testing Github2441: Add RDProps interface to Conformers. -37: [00:24:56] done -37: [00:24:56] ------------------------------------- -37: [00:24:56] Testing Issue2510: Pickle Confs as double. -37: [00:24:56] done -37: [00:24:56] ------------------------------------- -37: [00:24:56] Testing Github #2465: Negative atom-map numbers cause depickling to fail. -37: [00:24:56] done -37: [00:24:56] ------------------------------------- -37: [00:24:56] Testing loading pickled mols with conformers -37: [00:24:56] done -37: [00:24:56] ------------------------------------- -37: [00:24:56] Testing conformer reading/writing options -37: [00:24:56] done -37: [00:24:56] ------------------------------------- -37: [00:24:56] Testing property reading options -37: [00:24:56] done -37: [00:24:56] ------------------------------------- -37: [00:24:56] Testing property reading options -28: done -28: ------------------------------------- -28: Unit tests for copying UFF ForceFields. -28: done -28: ------------------------------------- -28: Unit test for UFF butane scan. -28: done -36: -------------------------- -36: -------------------------- -36: C/C=C/C(C)Cl -36: [00:24:56] Conflicting single bond directions around double bond at index 2. -36: [00:24:56] BondStereo set to STEREONONE and single bond directions set to NONE. -36: [00:24:56] Conflicting single bond directions around double bond at index 4. -36: [00:24:56] BondStereo set to STEREONONE and single bond directions set to NONE. -36: [00:24:56] Conflicting single bond directions around double bond at index 15. -36: [00:24:56] BondStereo set to STEREONONE and single bond directions set to NONE. -36: [00:24:56] Conflicting single bond directions around double bond at index 2. -36: [00:24:56] BondStereo set to STEREONONE and single bond directions set to NONE. -36: [00:24:56] Conflicting single bond directions around double bond at index 1. -36: [00:24:56] BondStereo set to STEREONONE and single bond directions set to NONE. -36: -------------------------------------------------- - 26/236 Test #36: graphmoltestChirality .................. Passed 0.25 sec -15: ......... -15: ---------------------------------------------------------------------- -15: Ran 9 tests in 0.007s -15: -15: OK - 27/236 Test #15: pySparseIntVect ........................ Passed 0.45 sec -13: ...... -13: ---------------------------------------------------------------------- -13: Ran 6 tests in 0.030s -13: -13: OK - 28/236 Test #43: molBundleTest .......................... Passed 0.22 sec - 29/236 Test #44: testSGroup ............................. Passed 0.22 sec - 30/236 Test #45: test-valgrind .......................... Passed 0.22 sec -46: Randomness seeded to: 1312583924 -46: [00:24:56] WARNING: not removing hydrogen atom without neighbors -46: [00:24:56] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -46: [00:24:56] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -46: [00:24:56] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -46: [00:24:56] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -46: [00:24:56] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -46: [00:24:56] Explicit valence for atom # 1 N, 5, is greater than permitted -46: [00:24:56] Explicit valence for atom # 1 N, 6, is greater than permitted -46: [00:24:56] Explicit valence for atom # 1 N, 5, is greater than permitted -46: [00:24:56] Explicit valence for atom # 1 N, 5, is greater than permitted -46: [00:24:56] Explicit valence for atom # 2 O, 3, is greater than permitted -46: [00:24:56] Explicit valence for atom # 2 O, 3, is greater than permitted -46: [00:24:56] non-ring atom 2 marked aromatic -46: [00:24:56] non-ring atom 2 marked aromatic -46: [00:24:56] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -46: [00:24:56] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -46: [00:24:56] Can't kekulize mol. Unkekulized atoms: 1 2 3 -46: [00:24:56] Can't kekulize mol. Unkekulized atoms: 1 2 3 -46: [00:24:56] Can't kekulize mol. Unkekulized atoms: 0 1 2 -46: [00:24:56] Can't kekulize mol. Unkekulized atoms: 0 1 2 -46: [00:24:56] Explicit valence for atom # 1 O, 3, is greater than permitted -46: [00:24:56] Explicit valence for atom # 4 F, 2, is greater than permitted -46: [00:24:56] Can't kekulize mol. Unkekulized atoms: 6 7 8 -46: [00:24:56] Explicit valence for atom # 1 C, 5, is greater than permitted -46: [00:24:56] WARNING: not removing hydrogen atom with dummy atom neighbors -46: [00:24:56] WARNING: not removing hydrogen atom with dummy atom neighbors -46: [00:24:56] WARNING: not removing hydrogen atom with wedged bond -46: [00:24:56] WARNING: not removing hydrogen atom without neighbors -46: [00:24:56] WARNING: not removing hydrogen atom without neighbors -46: [00:24:56] WARNING: not removing hydrogen atom without neighbors -46: [00:24:56] WARNING: not removing hydrogen atom without neighbors -46: [00:24:56] Unreasonable formal charge on atom # 0. -46: [00:24:56] -46: -46: **** -46: Pre-condition Violation -46: no atom -46: Violation occurred on line 181 in file ./Code/GraphMol/ROMol.cpp -46: Failed Expression: at -46: ---------- -46: Stacktrace: -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# 0x0000562EA1F90668 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000562EA1FDD938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000562EA1FDE458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000562EA1FDE8D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000562EA1FAFF43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000562EA1FB02AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000562EA1F2ADDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007FB7E5833CA8 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# 0x0000562EA1F2AE21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: ---------- -46: **** -46: -46: [00:24:56] -46: -46: **** -46: Pre-condition Violation -46: no owner -46: Violation occurred on line 153 in file ./Code/GraphMol/Atom.h -46: Failed Expression: dp_mol -46: ---------- -46: Stacktrace: -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# 0x0000562EA1F906F2 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000562EA1FDD938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000562EA1FDE458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000562EA1FDE8D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000562EA1FAFF43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000562EA1FB02AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000562EA1F2ADDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007FB7E5833CA8 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# 0x0000562EA1F2AE21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: ---------- -46: **** -46: -46: [00:24:56] -46: -46: **** -46: Pre-condition Violation -46: atom not associated with this molecule -46: Violation occurred on line 182 in file ./Code/GraphMol/ROMol.cpp -46: Failed Expression: &at->getOwningMol() == this -46: ---------- -46: Stacktrace: -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# 0x0000562EA1F90785 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000562EA1FDD938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000562EA1FDE458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000562EA1FDE8D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000562EA1FAFF43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000562EA1FB02AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000562EA1F2ADDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007FB7E5833CA8 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# 0x0000562EA1F2AE21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: ---------- -46: **** -46: -46: [00:24:56] -46: -46: **** -46: Pre-condition Violation -46: no atom -46: Violation occurred on line 364 in file ./Code/GraphMol/ROMol.cpp -46: Failed Expression: at -46: ---------- -46: Stacktrace: -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# 0x0000562EA1F90870 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000562EA1FDD938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000562EA1FDE458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000562EA1FDE8D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000562EA1FAFF43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000562EA1FB02AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000562EA1F2ADDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007FB7E5833CA8 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# 0x0000562EA1F2AE21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: ---------- -46: **** -46: -46: [00:24:56] -46: -46: **** -46: Pre-condition Violation -46: no owner -46: Violation occurred on line 153 in file ./Code/GraphMol/Atom.h -46: Failed Expression: dp_mol -46: ---------- -46: Stacktrace: -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# 0x0000562EA1F90901 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000562EA1FDD938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000562EA1FDE458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000562EA1FDE8D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000562EA1FAFF43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000562EA1FB02AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000562EA1F2ADDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007FB7E5833CA8 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# 0x0000562EA1F2AE21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: ---------- -46: **** -46: -46: [00:24:56] -46: -46: **** -46: Pre-condition Violation -46: atom not associated with this molecule -46: Violation occurred on line 365 in file ./Code/GraphMol/ROMol.cpp -46: Failed Expression: &at->getOwningMol() == this -46: ---------- -46: Stacktrace: -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# 0x0000562EA1F9099D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000562EA1FDD938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000562EA1FDE458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000562EA1FDE8D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000562EA1FAFF43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000562EA1FB02AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000562EA1F2ADDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007FB7E5833CA8 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# 0x0000562EA1F2AE21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: ---------- -46: **** -46: -46: [00:24:56] -46: -46: **** -46: Pre-condition Violation -46: no atom -46: Violation occurred on line 371 in file ./Code/GraphMol/ROMol.cpp -46: Failed Expression: at -46: ---------- -46: Stacktrace: -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# 0x0000562EA1F912B9 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000562EA1FDD938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000562EA1FDE458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000562EA1FDE8D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000562EA1FAFF43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000562EA1FB02AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000562EA1F2ADDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007FB7E5833CA8 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# 0x0000562EA1F2AE21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: ---------- -46: **** -46: -46: [00:24:56] -46: -46: **** -46: Pre-condition Violation -46: no owner -46: Violation occurred on line 153 in file ./Code/GraphMol/Atom.h -46: Failed Expression: dp_mol -46: ---------- -46: Stacktrace: -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# 0x0000562EA1F90B08 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000562EA1FDD938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000562EA1FDE458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000562EA1FDE8D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000562EA1FAFF43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000562EA1FB02AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000562EA1F2ADDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007FB7E5833CA8 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# 0x0000562EA1F2AE21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: ---------- -46: **** -46: -46: [00:24:56] -46: -46: **** -46: Pre-condition Violation -46: atom not associated with this molecule -46: Violation occurred on line 372 in file ./Code/GraphMol/ROMol.cpp -46: Failed Expression: &at->getOwningMol() == this -46: ---------- -46: Stacktrace: -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# 0x0000562EA1F90BA2 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000562EA1FDD938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000562EA1FDE458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000562EA1FDE8D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000562EA1FAFF43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000562EA1FB02AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000562EA1F2ADDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007FB7E5833CA8 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# 0x0000562EA1F2AE21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: ---------- -46: **** -46: -46: [00:24:56] -46: -46: **** -46: Pre-condition Violation -46: null atom passed in -46: Violation occurred on line 386 in file ./Code/GraphMol/ROMol.cpp -46: Failed Expression: atom_pin -46: ---------- -46: Stacktrace: -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# 0x0000562EA1F91291 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000562EA1FDD938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000562EA1FDE458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000562EA1FDE8D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000562EA1FAFF43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000562EA1FB02AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000562EA1F2ADDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007FB7E5833CA8 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# 0x0000562EA1F2AE21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: ---------- -46: **** -46: -46: [00:24:56] -46: -46: **** -46: Pre-condition Violation -46: cannot take ownership of an atom which already has an owner -46: Violation occurred on line 387 in file ./Code/GraphMol/ROMol.cpp -46: Failed Expression: !takeOwnership || !atom_pin->hasOwningMol() || &atom_pin->getOwningMol() == this -46: ---------- -46: Stacktrace: -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# 0x0000562EA1F90EB8 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000562EA1FDD938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000562EA1FDE458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000562EA1FDE8D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000562EA1FAFF43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000562EA1FB02AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000562EA1F2ADDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007FB7E5833CA8 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# 0x0000562EA1F2AE21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: ---------- -46: **** -46: -46: [00:24:56] -46: -46: **** -46: Pre-condition Violation -46: cannot take ownership of an bond which already has an owner -46: Violation occurred on line 412 in file ./Code/GraphMol/ROMol.cpp -46: Failed Expression: !takeOwnership || !bond_pin->hasOwningMol() || &bond_pin->getOwningMol() == this -46: ---------- -46: Stacktrace: -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# 0x0000562EA1F9126D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000562EA1FDD938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000562EA1FDE458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000562EA1FDE8D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000562EA1FAFF43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000562EA1FB02AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000562EA1F2ADDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007FB7E5833CA8 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# 0x0000562EA1F2AE21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: ---------- -46: **** -46: -46: [00:24:56] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -46: [00:24:56] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -46: [00:24:56] WARNING: not removing hydrogen atom without neighbors -46: [00:24:56] Explicit valence for atom # 1 F greater than permitted -46: [00:24:56] -46: -46: **** -46: Pre-condition Violation -46: plain atoms have no Query -46: Violation occurred on line 697 in file ./Code/GraphMol/Atom.cpp -46: Failed Expression: 0 -46: ---------- -46: Stacktrace: -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# 0x0000562EA1F3814B in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000562EA1FDD938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000562EA1FDE458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000562EA1FDE8D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000562EA1FAFF43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000562EA1FB02AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000562EA1F2ADDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007FB7E5833CA8 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# 0x0000562EA1F2AE21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: ---------- -46: **** -46: -46: [00:24:56] -46: -46: **** -46: Pre-condition Violation -46: plain atoms have no Query -46: Violation occurred on line 702 in file ./Code/GraphMol/Atom.cpp -46: Failed Expression: 0 -46: ---------- -46: Stacktrace: -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# 0x0000562EA1F381E0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000562EA1FDD938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000562EA1FDE458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000562EA1FDE8D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000562EA1FAFF43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000562EA1FB02AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000562EA1F2ADDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007FB7E5833CA8 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# 0x0000562EA1F2AE21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: ---------- -46: **** -46: -46: [00:24:56] -46: -46: **** -46: Pre-condition Violation -46: plain bonds have no Query -46: Violation occurred on line 207 in file ./Code/GraphMol/Bond.cpp -46: Failed Expression: 0 -46: ---------- -46: Stacktrace: -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# 0x0000562EA1F37E70 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000562EA1FDD938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000562EA1FDE458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000562EA1FDE8D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000562EA1FAFF43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000562EA1FB02AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000562EA1F2ADDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007FB7E5833CA8 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# 0x0000562EA1F2AE21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: ---------- -46: **** -46: -46: [00:24:56] -46: -46: **** -46: Pre-condition Violation -46: plain bonds have no query -46: Violation occurred on line 228 in file ./Code/GraphMol/Bond.cpp -46: Failed Expression: 0 -46: ---------- -46: Stacktrace: -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# 0x0000562EA1F37F05 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000562EA1FDD938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000562EA1FDE458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000562EA1FDE8D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000562EA1FAFF43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000562EA1FB02AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000562EA1F2ADDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007FB7E5833CA8 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# 0x0000562EA1F2AE21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: ---------- -46: **** -46: -46: [00:24:56] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -46: [00:24:56] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -46: [00:24:56] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -46: [00:24:56] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -46: [00:24:56] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -46: [00:24:56] Unusual charge on atom 0 number of radical electrons set to zero -46: [00:24:56] Unusual charge on atom 0 number of radical electrons set to zero -46: [00:24:56] Unusual charge on atom 0 number of radical electrons set to zero -46: [00:24:56] non-ring atom 0 marked aromatic -46: [00:24:56] non-ring atom 0 marked aromatic -46: [00:24:56] Explicit valence for atom # 1 C, 5, is greater than permitted -46: [00:24:56] Explicit valence for atom # 9 C, 5, is greater than permitted -46: [00:24:56] Explicit valence for atom # 3 N, 4, is greater than permitted -46: [00:24:56] Explicit valence for atom # 15 C, 5, is greater than permitted -46: [00:24:56] Explicit valence for atom # 11 C, 5, is greater than permitted -46: [00:24:56] Explicit valence for atom # 9 C, 5, is greater than permitted -46: [00:24:56] Explicit valence for atom # 9 C, 5, is greater than permitted -46: [00:24:56] Explicit valence for atom # 9 C, 6, is greater than permitted -46: [00:24:56] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -46: [00:24:56] Can't kekulize mol. Unkekulized atoms: 7 -46: [00:24:56] Can't kekulize mol. Unkekulized atoms: 3 -46: [00:24:56] Can't kekulize mol. Unkekulized atoms: 3 7 -46: [00:24:56] Can't kekulize mol. Unkekulized atoms: 3 7 -46: [00:24:56] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -46: [00:24:56] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -46: [00:24:56] Explicit valence for atom # 1 O, 3, is greater than permitted -46: [00:24:56] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -46: [00:24:56] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -46: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -46: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -46: [00:24:56] Invalid value for molAttachPoint: 4 on atom 1. Not expanding this atttachment point. -46: [00:24:56] Invalid value for _fromAttachPoint: -1 on atom 0. Not collapsing this atom -46: [00:24:56] Invalid value for _fromAttachPoint: 4 on atom 0. Not collapsing this atom -46: [00:24:56] non-ring atom 0 marked aromatic -46: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -46: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -46: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -46: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -46: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -46: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -46: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -46: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -46: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -46: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -46: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -46: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -46: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -47: Randomness seeded to: 4051697567 -47: =============================================================================== -47: All tests passed (62 assertions in 6 test cases) -47: - 31/236 Test #47: graphmolOrganometallicsCatch ........... Passed 0.22 sec -48: Randomness seeded to: 3794741203 -48: =============================================================================== -48: All tests passed (136 assertions in 8 test cases) -48: - 32/236 Test #48: graphmolSGroupCatch .................... Passed 0.21 sec -50: Randomness seeded to: 2424920200 -50: [00:24:56] unable to set wavy bonds for double bonds: 3 -50: [00:24:56] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -50: [00:24:56] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -50: [00:24:56] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. -50: [00:24:56] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. -50: [00:24:56] 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: 1285865515 -52: =============================================================================== -52: All tests passed (14 assertions in 4 test cases) -52: - 33/236 Test #52: moliteratorTestsCatch .................. Passed 0.21 sec -53: Randomness seeded to: 2879540123 -53: =============================================================================== -53: All tests passed (10 assertions in 1 test case) -53: - 34/236 Test #53: queryTestsCatch ........................ Passed 0.20 sec -54: Randomness seeded to: 1622115258 -54: =============================================================================== -54: All tests passed (6 assertions in 1 test case) -54: - 35/236 Test #54: molbundleTestsCatch .................... Passed 0.20 sec -55: Randomness seeded to: 1792630377 -55: =============================================================================== -55: All tests passed (45 assertions in 4 test cases) -55: - 36/236 Test #55: pickleTestsCatch ....................... Passed 0.20 sec -56: Randomness seeded to: 80509498 -56: =============================================================================== -56: All tests passed (7 assertions in 2 test cases) -56: - 37/236 Test #56: tableTestsCatch ........................ Passed 0.19 sec -57: Randomness seeded to: 2927609392 -57: =============================================================================== -57: All tests passed (230 assertions in 7 test cases) -57: - 38/236 Test #57: molopsTestsCatch ....................... Passed 0.19 sec -test 67 - Start 67: pyDepictor - -67: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Depictor/Wrap/testDepictor.py" -67: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/Wrap -67: Test timeout computed to be: 1500 -test 68 - Start 68: testMrvToMol - -68: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol -68: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse -68: Test timeout computed to be: 1500 -test 69 - Start 69: fileParsersTest1 - -69: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -69: Test timeout computed to be: 1500 -test 70 - Start 70: testAtropisomers - -70: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testAtropisomers -70: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -70: Test timeout computed to be: 1500 -test 71 - Start 71: testSquiggleDoubleBonds - -71: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testSquiggleDoubleBonds -71: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -71: Test timeout computed to be: 1500 -test 72 - Start 72: testMolSupplier - -72: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier -72: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -72: Test timeout computed to be: 1500 -test 73 - Start 73: testGeneralFileReader - -73: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testGeneralFileReader -73: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -73: Test timeout computed to be: 1500 -test 74 - Start 74: testMultithreadedMolSupplier - -74: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMultithreadedMolSupplier -74: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -74: Test timeout computed to be: 1500 -test 75 - Start 75: testMolWriter - -75: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolWriter -75: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -75: Test timeout computed to be: 1500 -test 76 - Start 76: testTplParser - -76: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testTplParser -76: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -76: Test timeout computed to be: 1500 -test 77 - Start 77: testMol2ToMol - -77: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMol2ToMol -77: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -77: Test timeout computed to be: 1500 -test 78 - Start 78: testSequence - -78: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testSequence -78: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -78: Test timeout computed to be: 1500 -test 79 - Start 79: testExtendedStereoParsing - -79: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testExtendedStereoParsing -79: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -79: Test timeout computed to be: 1500 -test 80 - Start 80: fileParsersCatchTest - -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 -37: [00:24:56] done -37: [00:24:56] ------------------------------------- -37: [00:24:56] Testing boost::serialization integration -37: [00:24:56] done -37: [00:24:56] ------------------------------------- -37: [00:24:56] Testing github issue 6036 -46: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -46: [00:24:56] Explicit valence for atom # 0 Al, 6, is greater than permitted -46: [00:24:56] Explicit valence for atom # 0 Al, 6, is greater than permitted -46: [00:24:56] Explicit valence for atom # 1 Si, 6, is greater than permitted -46: [00:24:56] Explicit valence for atom # 1 Si, 6, is greater than permitted -46: [00:24:56] Explicit valence for atom # 0 P, 6, is greater than permitted -46: [00:24:56] Explicit valence for atom # 0 P, 6, is greater than permitted -46: [00:24:56] Explicit valence for atom # 0 P, 7, is greater than permitted -46: [00:24:56] Explicit valence for atom # 0 P, 7, is greater than permitted -46: [00:24:56] Explicit valence for atom # 1 As, 6, is greater than permitted -46: [00:24:56] Explicit valence for atom # 1 As, 6, is greater than permitted -46: [00:24:56] Explicit valence for atom # 1 As, 7, is greater than permitted -46: [00:24:56] Explicit valence for atom # 1 As, 7, is greater than permitted -46: [00:24:56] Explicit valence for atom # 0 Sb, 6, is greater than permitted -46: [00:24:56] Explicit valence for atom # 0 Sb, 6, is greater than permitted -46: [00:24:56] Explicit valence for atom # 0 Sb, 7, is greater than permitted -46: [00:24:56] Explicit valence for atom # 0 Sb, 7, is greater than permitted -46: [00:24:56] Explicit valence for atom # 1 Bi, 6, is greater than permitted -46: [00:24:56] Explicit valence for atom # 1 Bi, 6, is greater than permitted -46: [00:24:56] Explicit valence for atom # 1 Bi, 8, is greater than permitted -46: [00:24:56] Explicit valence for atom # 1 Bi, 8, is greater than permitted -46: =============================================================================== -46: All tests passed (4479 assertions in 107 test cases) -46: -21: .................... -21: ---------------------------------------------------------------------- -21: Ran 20 tests in 0.039s -21: -21: OK -21: Testing Geometry wrapper -59: [00:24:56] SMILES Parse Error: Failed parsing SMILES 'CO' for input: 'CO' -59: [00:24:56] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' -59: [00:24:56] SMILES Parse Error: syntax error while parsing: - -59: [00:24:56] SMILES Parse Error: check for mistakes around position 1: -59: [00:24:56] - -59: [00:24:56] ^ -59: [00:24:56] SMILES Parse Error: Failed parsing SMILES '-' for input: '-' -59: [00:24:56] SMILES Parse Error: Failed parsing SMILES '[Bg]' for input: '[Bg]' -59: [00:24:56] SMILES Parse Error: Failed parsing SMILES 'C' for input: 'C' -59: [00:24:56] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' -59: [00:24:56] SMILES Parse Error: Failed parsing SMILES '*' for input: '*' -59: [00:24:56] SMARTS Parse Error: Failed parsing SMARTS 'CO' for input: 'CO' -59: [00:24:56] SMARTS Parse Error: Failed parsing SMARTS 'C-O' for input: 'C-O' -59: [00:24:56] SMARTS Parse Error: Failed parsing SMARTS '-' for input: '-' -59: [00:24:56] SMARTS Parse Error: Failed parsing SMARTS '[Bg]' for input: '[Bg]' -59: [00:24:56] SMARTS Parse Error: Failed parsing SMARTS 'C' for input: 'C' -59: [00:24:56] SMARTS Parse Error: Failed parsing SMARTS '-O' for input: '-O' -59: [00:24:56] SMARTS Parse Error: Failed parsing SMARTS '*' for input: '*' -25: ..... -25: ---------------------------------------------------------------------- -25: Ran 5 tests in 0.001s -25: -25: OK -25: Testing Alignment Wrapper code: -35: [00:24:56] non-ring atom 0 marked aromatic -35: [00:24:56] non-ring atom 0 marked aromatic -35: [00:24:56] Conflicting single bond directions around double bond at index 17. -35: [00:24:56] BondStereo set to STEREONONE and single bond directions set to NONE. -35: starting ring finding -35: done -35: starting ring finding -35: done -35: starting ring finding -35: done -35: C/C=N/c1ccc(cc1)c1cc2cc(c1)c1ccc(cc1)N=Cc1ccc(cc1)c1cc(cc(c1)c1ccc(cc1)C)c1ccc(cc1)C=Nc1ccc(cc1)c1cc(cc(c1)c1ccc(cc1)/N=C/C)c1ccc(cc1)N=Cc1ccc(cc1)c1cc(c3ccc(C=Nc4ccc(c5cc6c7ccc(N=Cc8ccc(c9cc(c%10ccc(C=Nc%11ccc2cc%11)cc%10)cc(c9)c2ccc(cc2)C=Nc2ccc(cc2)c2cc(cc(c2)c2ccc(cc2)N=Cc2ccc(cc2)c2cc(cc(c2)c2ccc(cc2)C)c2ccc(cc2)C=Nc2ccc(cc2)c2cc(c9ccc(N=Cc%10ccc(c%11cc(c%12ccc(C=Nc%13ccc(c(c6)c5)cc%13)cc%12)cc(c%11)c5ccc(cc5)C)cc%10)cc9)cc(c2)c2ccc(cc2)/N=C/C)c2ccc(cc2)/N=C/C)cc8)cc7)cc4)cc3)cc(c1)c1ccc(cc1)C -35: starting sanitization -35: done -35: starting sanitization -35: done -35: starting ring finding -35: done -35: starting ring finding -35: done -35: smiles: CC[C@]1(C(=O)c([nH])n)CC[C@](C)(O)CC1 -35: [00:24:56] WARNING: not removing hydrogen atom with dummy atom neighbors -35: ------------------------------- -35: [00:24:56] Explicit valence for atom # 0 N, 4, is greater than permitted -35: [00:24:56] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -35: [00:24:56] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -35: [00:24:56] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -35: [00:24:56] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -35: [00:24:56] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -35: [00:24:56] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -35: [00:24:56] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -35: [00:24:56] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -35: -35: [00:24:56] WARNING: not removing hydrogen atom with dummy atom neighbors -58: [00:24:56] WARNING: not removing hydrogen atom without neighbors -58: [00:24:56] WARNING: not removing hydrogen atom without neighbors -58: [00:24:56] WARNING: not removing hydrogen atom without neighbors -58: [00:24:56] WARNING: not removing hydrogen atom without neighbors -58: [00:24:56] WARNING: not removing hydrogen atom without neighbors -58: [00:24:56] WARNING: not removing hydrogen atom without neighbors -58: [00:24:56] WARNING: not removing hydrogen atom without neighbors -58: [00:24:56] WARNING: not removing hydrogen atom without neighbors -58: [00:24:56] WARNING: not removing hydrogen atom without neighbors -58: [00:24:56] WARNING: not removing hydrogen atom without neighbors -58: [00:24:56] WARNING: not removing hydrogen atom without neighbors -58: [00:24:56] Invalid chiral specification on atom 0 -58: [00:24:56] Invalid chiral specification on atom 0 -58: [00:24:56] Invalid chiral specification on atom 0 -58: [00:24:56] Invalid chiral specification on atom 0 -58: [00:24:56] Invalid chiral specification on atom 0 -58: [00:24:56] SMILES Parse Error: unclosed ring for input: 'C1.C11.C' -58: [00:24:56] 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: [00:24:56] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -58: [00:24:56] 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: [00:24:56] SMILES Parse Error: syntax error while parsing: c%()ccccc%() -58: [00:24:56] SMILES Parse Error: check for mistakes around position 4: -58: [00:24:56] c%()ccccc%() -58: [00:24:56] ~~~^ -58: [00:24:56] SMILES Parse Error: Failed parsing SMILES 'c%()ccccc%()' for input: 'c%()ccccc%()' -58: [00:24:56] SMILES Parse Error: syntax error while parsing: c%(100000)ccccc%(100000) -58: [00:24:56] SMILES Parse Error: check for mistakes around position 9: -58: [00:24:56] c%(100000)ccccc%(100000) -58: [00:24:56] ~~~~~~~~^ -58: [00:24:56] SMILES Parse Error: Failed parsing SMILES 'c%(100000)ccccc%(100000)' for input: 'c%(100000)ccccc%(100000)' -58: [00:24:56] SMILES Parse Error: duplicated ring closure 1 bonds atom 2 to itself for input: 'C1CC111' -58: [00:24:56] SMILES Parse Error: ring closure 1 duplicates bond between atom 0 and atom 1 for input: 'C1C1' -58: [00:24:56] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -58: [00:24:56] SMILES Parse Error: check for mistakes around position 14: -58: [00:24:56] COc(c1)cccc1C# -58: [00:24:56] ~~~~~~~~~~~~~^ -58: [00:24:56] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -58: [00:24:56] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -58: [00:24:56] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -58: [00:24:56] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -58: [00:24:56] SMILES Parse Error: check for mistakes around position 14: -58: [00:24:56] COc(c1)cccc1C# -58: [00:24:56] ~~~~~~~~~~~~~^ -58: [00:24:56] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -58: [00:24:56] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -58: [00:24:56] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -58: [00:24:56] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -58: [00:24:56] SMILES Parse Error: check for mistakes around position 14: -58: [00:24:56] COc(c1)cccc1C# -58: [00:24:56] ~~~~~~~~~~~~~^ -58: [00:24:56] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -58: [00:24:56] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -58: [00:24:56] 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: [00:24:56] SMILES Parse Error: extra close parentheses while parsing: C) -58: [00:24:56] SMILES Parse Error: check for mistakes around position 2: -58: [00:24:56] C) -58: [00:24:56] ~^ -58: [00:24:56] SMILES Parse Error: Failed parsing SMILES 'C)' for input: 'C)' -14: ...... -14: ---------------------------------------------------------------------- -14: Ran 6 tests in 0.001s -14: -14: OK -32: ...... -32: ---------------------------------------------------------------------- -32: Ran 6 tests in 0.001s -32: -32: OK -49: Randomness seeded to: 2391000526 -49: =============================================================================== -49: All tests passed (292 assertions in 12 test cases) -49: -40: [00:24:56] sorting (hanoi sort) vectors -2: .... -2: ---------------------------------------------------------------------- -2: Ran 4 tests in 0.019s -2: -2: OK -61: [00:24:56] SMARTS Parse Error: syntax error while parsing: [C:10H3]CC -61: [00:24:56] SMARTS Parse Error: Failed parsing SMARTS '[C:10H3]CC' for input: '[C:10H3]CC' -61: [00:24:56] SMARTS Parse Error: syntax error while parsing: [C:10:3]ON -61: [00:24:56] SMARTS Parse Error: Failed parsing SMARTS '[C:10:3]ON' for input: '[C:10:3]ON' -61: [00:24:56] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -61: [00:24:56] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -62: Randomness seeded to: 1220115536 -62: [00:24:56] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -62: [00:24:56] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -62: [00:24:56] SMARTS Parse Error: unclosed ring for input: 'c1ccccc' -62: [00:24:56] SMARTS Parse Error: unclosed ring for input: 'C1C' -62: [00:24:56] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -62: [00:24:56] SMARTS Parse Error: syntax error while parsing: C)foo -62: [00:24:56] SMARTS Parse Error: Failed parsing SMARTS 'C)foo' for input: 'C)foo' -62: [00:24:56] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| -62: [00:24:56] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$|' for input: 'CCC |$foo;;bar$|' -62: [00:24:56] unrecognized CXSMILES CONNECT value: 'EU'. Assuming 'eu' -62: [00:24:56] w block attempts to set wedging on bond 0 more than once. -62: [00:24:56] improperly formatted w block -62: [00:24:56] atom 3 is not associated with bond 1(1-2) in w block -62: [00:24:56] -62: -62: **** -62: Range Error -62: idx -62: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp -62: Failed Expression: 20 < 20 -62: ---------- -62: Stacktrace: -62: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -62: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -62: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -62: 3# RDKit::Canon::canonicalizeFragment(RDKit::ROMol&, int, std::vector >&, std::vector > const&, std::vector >&, boost::dynamic_bitset > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*, bool, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -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# 0x0000563FE2A31A5D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 8# 0x0000563FE2A82D28 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 9# 0x0000563FE2A83848 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 10# 0x0000563FE2A83CC0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 11# 0x0000563FE2A55303 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 12# 0x0000563FE2A5566C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 13# 0x0000563FE29E6E1E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 14# 0x00007F8528433CA8 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# 0x0000563FE29E6E61 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: ---------- -62: **** -62: -62: [00:24:56] +37: [20:24:12] done +37: [20:24:12] ------------------------------------- +37: [20:24:12] Testing sf.net issue 280. +37: [20:24:12] done +37: [20:24:12] ------------------------------------- +37: [20:24:12] Testing sf.net issue 285. +37: [20:24:12] done +37: [20:24:12] done +37: [20:24:12] done +37: [20:24:12] done +37: [20:24:12] done +37: [20:24:12] done +37: [20:24:12] done +37: [20:24:12] ------------------------------------- +37: [20:24:12] Testing Github2441: Add RDProps interface to Conformers. +37: [20:24:12] done +37: [20:24:12] ------------------------------------- +37: [20:24:12] Testing Issue2510: Pickle Confs as double. +37: [20:24:12] done +37: [20:24:12] ------------------------------------- +37: [20:24:12] Testing Github #2465: Negative atom-map numbers cause depickling to fail. +37: [20:24:12] done +37: [20:24:12] ------------------------------------- +37: [20:24:12] Testing loading pickled mols with conformers +37: [20:24:12] done +37: [20:24:12] ------------------------------------- +37: [20:24:12] Testing conformer reading/writing options +37: [20:24:12] done +37: [20:24:12] ------------------------------------- +37: [20:24:12] Testing property reading options +37: [20:24:12] done +37: [20:24:12] ------------------------------------- +37: [20:24:12] Testing property reading options +37: [20:24:12] done +37: [20:24:12] ------------------------------------- +37: [20:24:12] Testing boost::serialization integration +37: [20:24:12] done +37: [20:24:12] ------------------------------------- +37: [20:24:12] Testing github issue 6036 +70: [20:24:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [20:24:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [20:24:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [20:24:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [20:24:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [20:24:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [20:24:12] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +70: [20:24:12] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +70: [20:24:12] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +70: [20:24:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [20:24:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [20:24:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [20:24:12] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +70: [20:24:12] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +70: [20:24:12] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +62: [20:24:12] w block attempts to set wedging on bond 0 more than once. +62: [20:24:12] improperly formatted w block +62: [20:24:12] atom 3 is not associated with bond 1(1-2) in w block +62: [20:24:12] 62: 62: **** 62: Range Error @@ -18005,92 +18077,24 @@ 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# 0x0000563FE2A31A5D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 8# 0x0000563FE2A82D28 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 9# 0x0000563FE2A83848 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 10# 0x0000563FE2A83CC0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 11# 0x0000563FE2A55303 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 12# 0x0000563FE2A5566C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 13# 0x0000563FE29E6E1E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 14# 0x00007F8528433CA8 in /lib/x86_64-linux-gnu/libc.so.6 +62: 7# 0x000055A19838CA5D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 8# 0x000055A1983DDD28 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 9# 0x000055A1983DE848 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 10# 0x000055A1983DECC0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 11# 0x000055A1983B0303 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 12# 0x000055A1983B066C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 13# 0x000055A198341E1E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 14# 0x00007FA8A5C33CA8 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# 0x0000563FE29E6E61 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 16# 0x000055A198341E61 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch 62: ---------- 62: **** 62: -62: [00:24:56] SMARTS Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5' -62: [00:24:56] SMILES Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5' -62: [00:24:56] SMARTS Parse Error: syntax error while parsing: C1C)foo -62: [00:24:56] SMARTS Parse Error: Failed parsing SMARTS 'C1C)foo' for input: 'C1C)foo' -62: [00:24:56] SMILES Parse Error: extra close parentheses while parsing: C1C)foo -62: [00:24:56] SMILES Parse Error: check for mistakes around position 4: -62: [00:24:56] C1C)foo -62: [00:24:56] ~~~^ -62: [00:24:56] 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: 3848582170 -63: [00:24:56] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -63: [00:24:56] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -63: [00:24:56] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -63: [00:24:56] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -63: [00:24:56] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -63: [00:24:56] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -63: [00:24:56] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -63: [00:24:56] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -63: [00:24:56] 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: 483056532 -64: =============================================================================== -64: All tests passed (14 assertions in 2 test cases) -64: - 39/236 Test #13: pyDiscreteValueVect .................... Passed 0.50 sec - 40/236 Test #14: pyRealValueVect ........................ Passed 0.50 sec - 41/236 Test #21: testPyGeometry ......................... Passed 0.36 sec - 42/236 Test #25: pyAlignment ............................ Passed 0.35 sec - 43/236 Test #28: testUFFForceField ...................... Passed 0.35 sec - 44/236 Test #32: pyDistGeom ............................. Passed 0.31 sec - 45/236 Test #37: graphmoltestPickler .................... Passed 0.29 sec - 46/236 Test #49: graphmolAdjustQueryCatch ............... Passed 0.26 sec - 47/236 Test #50: chiralityTestsCatch .................... Passed 0.26 sec - 48/236 Test #59: smiTest2 ............................... Passed 0.18 sec - 49/236 Test #61: smaTest1 ............................... Passed 0.17 sec - 50/236 Test #62: smiTestCatch ........................... Passed 0.17 sec - 51/236 Test #63: nontetrahedralCatch .................... Passed 0.17 sec - 52/236 Test #64: v2smiTestCatch ......................... Passed 0.12 sec -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 -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 +28: done + 46/236 Test #25: pyAlignment ............................ Passed 0.26 sec + 47/236 Test #28: testUFFForceField ...................... Passed 0.26 sec + 48/236 Test #32: pyDistGeom ............................. Passed 0.26 sec + 49/236 Test #76: testTplParser .......................... Passed 0.07 sec test 86 Start 86: v2MolSuppliers @@ -18115,45 +18119,28 @@ 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 - 53/236 Test #46: graphmolTestsCatch ..................... Passed 0.33 sec - 54/236 Test #58: smiTest1 ............................... Passed 0.30 sec - 55/236 Test #2: pyCoordGen ............................. Passed 0.58 sec -66: Randomness seeded to: 380987438 -66: =============================================================================== -66: All tests passed (580 assertions in 18 test cases) -66: - 56/236 Test #66: depictorCatch .......................... Passed 0.18 sec -60: Randomness seeded to: 2956600201 + 50/236 Test #37: graphmoltestPickler .................... Passed 0.26 sec + 51/236 Test #77: testMol2ToMol .......................... Passed 0.08 sec +72: [20:24:12] Ignoring invalid chirality label: '2_bad_chirality' +61: [20:24:12] SMARTS Parse Error: syntax error while parsing: [C:10H3]CC +61: [20:24:12] SMARTS Parse Error: Failed parsing SMARTS '[C:10H3]CC' for input: '[C:10H3]CC' +61: [20:24:12] SMARTS Parse Error: syntax error while parsing: [C:10:3]ON +61: [20:24:12] SMARTS Parse Error: Failed parsing SMARTS '[C:10:3]ON' for input: '[C:10:3]ON' +61: [20:24:12] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +61: [20:24:12] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged + 52/236 Test #61: smaTest1 ............................... Passed 0.18 sec +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 + 53/236 Test #2: pyCoordGen ............................. Passed 0.32 sec +21: .................... +21: ---------------------------------------------------------------------- +21: Ran 20 tests in 0.069s +21: +21: OK +21: Testing Geometry wrapper +60: Randomness seeded to: 3601242379 60: Test 60: 60: ShortAtropisomerNoCoords.cxsmi @@ -18214,16 +18201,16 @@ 60: 60: BMS-986142_atrop5.cxsmi 60: -60: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [20:24:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [20:24:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [20:24:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [20:24:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [20:24:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [20:24:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [20:24:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [20:24:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [20:24:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [20:24:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 60: Test 60: 60: BMS-986142_atrop6.cxsmi @@ -18232,280 +18219,583 @@ 60: 60: BMS-986142_atropBad1.cxsmi 60: -60: [00:24:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -60: [00:24:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -60: [00:24:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -60: [00:24:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -60: [00:24:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +60: [20:24:12] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +60: [20:24:12] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +60: [20:24:12] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +60: [20:24:12] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +60: [20:24:12] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 60: Test 60: 60: BMS-986142_atropBad2.cxsmi 60: -60: [00:24:56] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -60: [00:24:56] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -60: [00:24:56] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -60: [00:24:56] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -60: [00:24:56] 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: [00:24:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -60: [00:24:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -60: [00:24:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -60: [00:24:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -60: [00:24:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -30: ...[00:24:56] Molecule does not have explicit Hs. Consider calling AddHs() -68: Using new chirality perception -68: Test -68: -68: rxnStereoMarkedCrossed.mrv -68: -68: Test -68: -68: 145323811.mol -68: -68: [00:24:56] 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: [00:24:56] For a MultipleSgroup expansion, the matching orphaned bond was not found -68: The multiple sgroup will be ignored -69: *************************************** -69: *************************************** -69: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: [00:24:56] bond with order 0 found on line 7. This is not part of the MDL specification. -69: [00:24:56] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) -69: [00:24:56] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) -69: [00:24:56] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -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 -70: [00:24:56] ---- Running with POSIX locale ----- -70: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [00:24:56] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 -70: [00:24:56] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 -70: [00:24:56] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 -70: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [00:24:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 -70: [00:24:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 -70: [00:24:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 -70: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [00:24:56] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 -70: [00:24:56] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 -70: [00:24:56] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 -70: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [00:24:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -70: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [00:24:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -70: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [00:24:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -70: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [00:24:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 -70: [00:24:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 -70: [00:24:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 -70: [00:24:56] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -70: [00:24:56] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -70: [00:24:56] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -70: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [00:24:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -70: [00:24:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -70: [00:24:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -70: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -71: Randomness seeded to: 1493351579 -71: =============================================================================== -71: All tests passed (15 assertions in 3 test cases) -71: - 57/236 Test #71: testSquiggleDoubleBonds ................ Passed 0.11 sec -72: [00:24:56] -72: ----------------------------------------- -72: [00:24:56] Ignoring invalid chirality label: '2_bad_chirality' -73: [00:24:56] -73: ----------------------------------------- -73: [00:24:56] Finished: testDetermineFormat() -73: [00:24:56] ----------------------------------------- -73: -73: [00:24:56] -73: ----------------------------------------- -73: [00:24:56] Finished: testSdf() -73: [00:24:56] ----------------------------------------- -73: -73: [00:24:56] -73: ----------------------------------------- -73: [00:24:56] Finished: testSmi() -73: [00:24:56] ----------------------------------------- -73: -73: [00:24:56] -73: ----------------------------------------- -73: [00:24:56] Finished: testMae() -73: [00:24:56] ----------------------------------------- -73: -73: [00:24:56] -73: ----------------------------------------- -73: [00:24:56] Finished: testTdt() -73: [00:24:56] ----------------------------------------- -73: -74: [00:24:56] -74: ----------------------------------------- -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 -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 -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: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [00:24:56] 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: [00:24:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +60: [20:24:12] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 + 54/236 Test #79: testExtendedStereoParsing .............. Passed 0.07 sec + 55/236 Test #16: pyFPB .................................. Passed 0.31 sec +81: Randomness seeded to: 2645307379 +81: =============================================================================== +81: All tests passed (95 assertions in 4 test cases) +81: + 56/236 Test #81: testPropertyLists ...................... Passed 0.07 sec +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: [20:24:12] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +58: [20:24:12] 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: [20:24:12] SMILES Parse Error: syntax error while parsing: c%()ccccc%() +58: [20:24:12] SMILES Parse Error: check for mistakes around position 4: +58: [20:24:12] c%()ccccc%() +58: [20:24:12] ~~~^ +58: [20:24:12] SMILES Parse Error: Failed parsing SMILES 'c%()ccccc%()' for input: 'c%()ccccc%()' +58: [20:24:12] SMILES Parse Error: syntax error while parsing: c%(100000)ccccc%(100000) +58: [20:24:12] SMILES Parse Error: check for mistakes around position 9: +58: [20:24:12] c%(100000)ccccc%(100000) +58: [20:24:12] ~~~~~~~~^ +58: [20:24:12] SMILES Parse Error: Failed parsing SMILES 'c%(100000)ccccc%(100000)' for input: 'c%(100000)ccccc%(100000)' +58: [20:24:12] SMILES Parse Error: duplicated ring closure 1 bonds atom 2 to itself for input: 'C1CC111' +58: [20:24:12] SMILES Parse Error: ring closure 1 duplicates bond between atom 0 and atom 1 for input: 'C1C1' +58: [20:24:12] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +58: [20:24:12] SMILES Parse Error: check for mistakes around position 14: +58: [20:24:12] COc(c1)cccc1C# +58: [20:24:12] ~~~~~~~~~~~~~^ +58: [20:24:12] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +58: [20:24:12] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +58: [20:24:12] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +58: [20:24:12] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +58: [20:24:12] SMILES Parse Error: check for mistakes around position 14: +58: [20:24:12] COc(c1)cccc1C# +58: [20:24:12] ~~~~~~~~~~~~~^ +58: [20:24:12] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +58: [20:24:12] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +58: [20:24:12] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +58: [20:24:12] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +58: [20:24:12] SMILES Parse Error: check for mistakes around position 14: +58: [20:24:12] COc(c1)cccc1C# +58: [20:24:12] ~~~~~~~~~~~~~^ +58: [20:24:12] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +58: [20:24:12] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +58: [20:24:12] 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: [20:24:12] SMILES Parse Error: extra close parentheses while parsing: C) +58: [20:24:12] SMILES Parse Error: check for mistakes around position 2: +58: [20:24:12] C) +58: [20:24:12] ~^ +58: [20:24:12] SMILES Parse Error: Failed parsing SMILES 'C)' for input: 'C)' +80: Randomness seeded to: 134009864 +80: [20:24:12] SGroup SAP line too short: 'M SAP 1 1 8' on line 29 +80: [20:24:12] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 +80: [20:24:12] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +80: [20:24:12] SGroup 1 is invalid and will be ignored +80: [20:24:12] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 +80: [20:24:12] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +80: [20:24:12] SGroup 1 is invalid and will be ignored +80: [20:24:12] SGroup SAP line too short: 'M SAP 1 1 8' on line 35 +80: [20:24:12] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 +80: [20:24:12] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 +80: [20:24:12] SGroup SAP line too short: 'M SAP 2 1 12' on line 38 +80: [20:24:12] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +80: [20:24:12] SGroup 1 is invalid and will be ignored +80: [20:24:12] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 +80: [20:24:12] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 +80: [20:24:12] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +80: [20:24:12] SGroup 1 is invalid and will be ignored +80: [20:24:12] SGroup 3 referenced on line 40 not found. +80: [20:24:12] +80: +80: **** +80: Pre-condition Violation +80: no bonds +80: Violation occurred on line 181 in file ./Code/GraphMol/SubstanceGroup.cpp +80: Failed Expression: !d_bonds.empty() +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::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# 0x00007FC76B6DA81E 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# 0x0000556E854DE6A9 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x0000556E85556228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000556E85556D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000556E855571C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000556E855288C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000556E85528C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000556E8549BC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x00007FC76AC33CA8 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# 0x0000556E8549BC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: ---------- +80: **** +80: +80: [20:24:12] SGroup 3 referenced on line 40 not found. +80: [20:24:12] +80: +80: **** +80: Pre-condition Violation +80: no bonds +80: Violation occurred on line 181 in file ./Code/GraphMol/SubstanceGroup.cpp +80: Failed Expression: !d_bonds.empty() +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::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# 0x00007FC76B6DA81E 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# 0x0000556E854DE752 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x0000556E85556228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000556E85556D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000556E855571C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000556E855288C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000556E85528C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000556E8549BC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x00007FC76AC33CA8 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# 0x0000556E8549BC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: ---------- +80: **** +80: +80: [20:24:12] no bonds +80: [20:24:12] SGroup 1 is invalid and will be ignored +80: [20:24:12] SGroup line too short: 'M SBV 1 6' on line 42 +80: [20:24:12] SGroup 1 is invalid and will be ignored +80: [20:24:12] SGroup line too short: 'M SBL 2 3 9 10' on line 46 +80: [20:24:12] SGroup 2 is invalid and will be ignored +80: [20:24:12] +80: +80: **** +80: Pre-condition Violation +80: bookmark not found +80: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp +80: Failed Expression: (lu != d_bondBookmarks.end()) +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::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# 0x00007FC76B6DA6AB 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# 0x0000556E854DF312 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000556E85556228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000556E85556D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000556E855571C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000556E855288C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000556E85528C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000556E8549BC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x00007FC76AC33CA8 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# 0x0000556E8549BC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: ---------- +80: **** +80: +80: [20:24:12] +80: +80: **** +80: Pre-condition Violation +80: bookmark not found +80: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp +80: Failed Expression: (lu != d_bondBookmarks.end()) +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::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# 0x00007FC76B6DA6AB 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# 0x0000556E854DF3BA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000556E85556228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000556E85556D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000556E855571C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000556E855288C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000556E85528C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000556E8549BC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x00007FC76AC33CA8 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# 0x0000556E8549BC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: ---------- +80: **** +80: +80: [20:24:12] bookmark not found +80: [20:24:12] +80: +80: **** +80: Pre-condition Violation +80: bond is not part of the SubstanceGroup +80: Violation occurred on line 200 in file ./Code/GraphMol/SubstanceGroup.cpp +80: Failed Expression: std::find(d_bonds.begin(), d_bonds.end(), bondIdx) != d_bonds.end() +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::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# 0x00007FC76B6DA81E 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# 0x0000556E854DF3BA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000556E85556228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000556E85556D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000556E855571C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000556E855288C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000556E85528C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000556E8549BC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x00007FC76AC33CA8 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# 0x0000556E8549BC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: ---------- +80: **** +80: +80: [20:24:12] bond is not part of the SubstanceGroup +80: [20:24:12] SGroup 2 is invalid and will be ignored +80: [20:24:12] +80: +80: **** +80: Pre-condition Violation +80: bookmark not found +80: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp +80: Failed Expression: (lu != d_atomBookmarks.end()) +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::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# 0x00007FC76B6DA6AB 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# 0x0000556E854DF729 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000556E85556228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000556E85556D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000556E855571C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000556E855288C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000556E85528C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000556E8549BC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x00007FC76AC33CA8 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# 0x0000556E8549BC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: ---------- +80: **** +80: +80: [20:24:12] +80: +80: **** +80: Pre-condition Violation +80: bookmark not found +80: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp +80: Failed Expression: (lu != d_atomBookmarks.end()) +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::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# 0x00007FC76B6DA6AB 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# 0x0000556E854DF7D1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000556E85556228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000556E85556D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000556E855571C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000556E855288C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000556E85528C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000556E8549BC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x00007FC76AC33CA8 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# 0x0000556E8549BC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: ---------- +80: **** +80: +80: [20:24:12] bookmark not found +80: [20:24:12] Neither beginning nor ending atoms of bond 9 is in this SubstanceGroup. +80: [20:24:12] SGroup 2 is invalid and will be ignored +80: [20:24:12] WARNING: final character of V3000 array is not ')' +80: [20:24:12] +80: +80: **** +80: Pre-condition Violation +80: bookmark not found +80: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp +80: Failed Expression: (lu != d_bondBookmarks.end()) +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::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::ParseV3000ParseLabel(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_stringstream, std::allocator >&, std::vector, std::allocator >, std::allocator, std::allocator > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) 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# 0x0000556E854DD033 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000556E85556228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000556E85556D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000556E855571C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000556E855288C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000556E85528C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000556E8549BC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x00007FC76AC33CA8 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# 0x0000556E8549BC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: ---------- +80: **** +80: +80: [20:24:12] WARNING: final character of V3000 array is not ')' +80: [20:24:12] +80: +80: **** +80: Pre-condition Violation +80: bookmark not found +80: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp +80: Failed Expression: (lu != d_bondBookmarks.end()) +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::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::ParseV3000ParseLabel(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_stringstream, std::allocator >&, std::vector, std::allocator >, std::allocator, std::allocator > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) 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# 0x0000556E854DD0CB in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000556E85556228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000556E85556D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000556E855571C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000556E855288C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000556E85528C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000556E8549BC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x00007FC76AC33CA8 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# 0x0000556E8549BC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: ---------- +80: **** +80: +80: [20:24:12] bookmark not found +80: [20:24:12] SGroup 1 is invalid and will be ignored +80: [20:24:12] WARNING: final character of V3000 array is not ')' +80: [20:24:12] +80: +80: **** +80: Pre-condition Violation +80: bookmark not found +80: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp +80: Failed Expression: (lu != d_atomBookmarks.end()) +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::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::ParseV3000ParseLabel(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_stringstream, std::allocator >&, std::vector, std::allocator >, std::allocator, std::allocator > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) 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# 0x0000556E854DD434 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000556E85556228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000556E85556D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000556E855571C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000556E855288C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000556E85528C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000556E8549BC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x00007FC76AC33CA8 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# 0x0000556E8549BC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: ---------- +80: **** +80: +80: [20:24:12] WARNING: final character of V3000 array is not ')' +80: [20:24:12] +80: +80: **** +80: Pre-condition Violation +80: bookmark not found +80: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp +80: Failed Expression: (lu != d_atomBookmarks.end()) +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::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::ParseV3000ParseLabel(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_stringstream, std::allocator >&, std::vector, std::allocator >, std::allocator, std::allocator > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) 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# 0x0000556E854DD4CC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000556E85556228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000556E85556D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000556E855571C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000556E855288C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000556E85528C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000556E8549BC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x00007FC76AC33CA8 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# 0x0000556E8549BC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: ---------- +80: **** +80: +80: [20:24:12] bookmark not found +80: [20:24:12] SGroup 1 is invalid and will be ignored +80: [20:24:12] +80: +80: **** +80: Pre-condition Violation +80: bookmark not found +80: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp +80: Failed Expression: (lu != d_bondBookmarks.end()) +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::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::ParseV3000ParseLabel(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_stringstream, std::allocator >&, std::vector, std::allocator >, std::allocator, std::allocator > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) 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# 0x0000556E854DD833 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000556E85556228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000556E85556D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000556E855571C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000556E855288C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000556E85528C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000556E8549BC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x00007FC76AC33CA8 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# 0x0000556E8549BC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: ---------- +80: **** +80: +80: [20:24:12] +80: +80: **** +80: Pre-condition Violation +80: bookmark not found +80: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp +80: Failed Expression: (lu != d_bondBookmarks.end()) +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::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::ParseV3000ParseLabel(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_stringstream, std::allocator >&, std::vector, std::allocator >, std::allocator, std::allocator > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) 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# 0x0000556E854DD8CC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000556E85556228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000556E85556D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000556E855571C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000556E855288C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000556E85528C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000556E8549BC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x00007FC76AC33CA8 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# 0x0000556E8549BC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: ---------- +80: **** +80: +80: [20:24:12] bookmark not found +80: [20:24:12] SGroup 2 is invalid and will be ignored +80: [20:24:12] +80: +80: **** +80: Pre-condition Violation +80: bookmark not found +80: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp +80: Failed Expression: (lu != d_atomBookmarks.end()) +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::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::ParseV3000ParseLabel(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_stringstream, std::allocator >&, std::vector, std::allocator >, std::allocator, std::allocator > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) 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# 0x0000556E854DDC32 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000556E85556228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000556E85556D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000556E855571C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000556E855288C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000556E85528C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000556E8549BC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x00007FC76AC33CA8 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# 0x0000556E8549BC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: ---------- +80: **** +80: +80: [20:24:12] +80: +80: **** +80: Pre-condition Violation +80: bookmark not found +80: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp +80: Failed Expression: (lu != d_atomBookmarks.end()) +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::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::ParseV3000ParseLabel(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_stringstream, std::allocator >&, std::vector, std::allocator >, std::allocator, std::allocator > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) 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# 0x0000556E854DDCCC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000556E85556228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000556E85556D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000556E855571C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000556E855288C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000556E85528C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000556E8549BC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x00007FC76AC33CA8 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# 0x0000556E8549BC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: ---------- +80: **** +80: +80: [20:24:12] bookmark not found +80: [20:24:12] SGroup 2 is invalid and will be ignored +80: [20:24:12] Explicit valence for atom # 2 O, 3, is greater than permitted +80: [20:24:12] Explicit valence for atom # 1 O, 3, is greater than permitted +80: [20:24:12] Explicit valence for atom # 1 C, 5, is greater than permitted +80: [20:24:12] sanitize [20:24:12] UNK: [20:24:12] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 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 @@ -19490,650 +19780,271 @@ 78: CONECT 27 28 28 29 78: END 78: -80: Randomness seeded to: 3940938489 -80: [00:24:56] SGroup SAP line too short: 'M SAP 1 1 8' on line 29 -80: [00:24:56] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 -80: [00:24:56] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -80: [00:24:56] SGroup 1 is invalid and will be ignored -80: [00:24:56] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 -80: [00:24:56] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -80: [00:24:56] SGroup 1 is invalid and will be ignored -80: [00:24:56] SGroup SAP line too short: 'M SAP 1 1 8' on line 35 -80: [00:24:56] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 -80: [00:24:56] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 -80: [00:24:56] SGroup SAP line too short: 'M SAP 2 1 12' on line 38 -80: [00:24:56] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -80: [00:24:56] SGroup 1 is invalid and will be ignored -80: [00:24:56] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 -80: [00:24:56] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 -80: [00:24:56] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -80: [00:24:56] SGroup 1 is invalid and will be ignored -80: [00:24:56] SGroup 3 referenced on line 40 not found. -80: [00:24:56] -80: -80: **** -80: Pre-condition Violation -80: no bonds -80: Violation occurred on line 181 in file ./Code/GraphMol/SubstanceGroup.cpp -80: Failed Expression: !d_bonds.empty() -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::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# 0x00007F71A42DA81E 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# 0x0000556AE99056A9 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x0000556AE997D228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000556AE997DD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000556AE997E1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000556AE994F8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000556AE994FC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000556AE98C2C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x00007F71A3833CA8 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# 0x0000556AE98C2C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: ---------- -80: **** -80: -80: [00:24:56] SGroup 3 referenced on line 40 not found. -80: [00:24:56] -80: -80: **** -80: Pre-condition Violation -80: no bonds -80: Violation occurred on line 181 in file ./Code/GraphMol/SubstanceGroup.cpp -80: Failed Expression: !d_bonds.empty() -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::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# 0x00007F71A42DA81E 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# 0x0000556AE9905752 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x0000556AE997D228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000556AE997DD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000556AE997E1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000556AE994F8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000556AE994FC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000556AE98C2C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x00007F71A3833CA8 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# 0x0000556AE98C2C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: ---------- -80: **** -80: -80: [00:24:56] no bonds -80: [00:24:56] SGroup 1 is invalid and will be ignored -80: [00:24:56] SGroup line too short: 'M SBV 1 6' on line 42 -80: [00:24:56] SGroup 1 is invalid and will be ignored -80: [00:24:56] SGroup line too short: 'M SBL 2 3 9 10' on line 46 -80: [00:24:56] SGroup 2 is invalid and will be ignored -80: [00:24:56] -80: -80: **** -80: Pre-condition Violation -80: bookmark not found -80: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp -80: Failed Expression: (lu != d_bondBookmarks.end()) -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::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# 0x00007F71A42DA6AB 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# 0x0000556AE9906312 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000556AE997D228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000556AE997DD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000556AE997E1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000556AE994F8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000556AE994FC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000556AE98C2C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x00007F71A3833CA8 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# 0x0000556AE98C2C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: ---------- -80: **** -80: -80: [00:24:56] -80: -80: **** -80: Pre-condition Violation -80: bookmark not found -80: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp -80: Failed Expression: (lu != d_bondBookmarks.end()) -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::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# 0x00007F71A42DA6AB 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# 0x0000556AE99063BA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000556AE997D228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000556AE997DD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000556AE997E1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000556AE994F8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000556AE994FC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000556AE98C2C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x00007F71A3833CA8 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# 0x0000556AE98C2C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: ---------- -80: **** -80: -80: [00:24:56] bookmark not found -80: [00:24:56] -80: -80: **** -80: Pre-condition Violation -80: bond is not part of the SubstanceGroup -80: Violation occurred on line 200 in file ./Code/GraphMol/SubstanceGroup.cpp -80: Failed Expression: std::find(d_bonds.begin(), d_bonds.end(), bondIdx) != d_bonds.end() -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::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# 0x00007F71A42DA81E 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# 0x0000556AE99063BA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000556AE997D228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000556AE997DD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000556AE997E1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000556AE994F8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000556AE994FC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000556AE98C2C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x00007F71A3833CA8 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# 0x0000556AE98C2C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: ---------- -80: **** -80: -80: [00:24:56] bond is not part of the SubstanceGroup -80: [00:24:56] SGroup 2 is invalid and will be ignored -80: [00:24:56] -80: -80: **** -80: Pre-condition Violation -80: bookmark not found -80: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp -80: Failed Expression: (lu != d_atomBookmarks.end()) -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::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# 0x00007F71A42DA6AB 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# 0x0000556AE9906729 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000556AE997D228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000556AE997DD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000556AE997E1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000556AE994F8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000556AE994FC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000556AE98C2C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x00007F71A3833CA8 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# 0x0000556AE98C2C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: ---------- -80: **** -80: -80: [00:24:56] -80: -80: **** -80: Pre-condition Violation -80: bookmark not found -80: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp -80: Failed Expression: (lu != d_atomBookmarks.end()) -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::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# 0x00007F71A42DA6AB 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# 0x0000556AE99067D1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000556AE997D228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000556AE997DD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000556AE997E1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000556AE994F8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000556AE994FC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000556AE98C2C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x00007F71A3833CA8 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# 0x0000556AE98C2C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: ---------- -80: **** -80: -80: [00:24:56] bookmark not found -80: [00:24:56] Neither beginning nor ending atoms of bond 9 is in this SubstanceGroup. -80: [00:24:56] SGroup 2 is invalid and will be ignored -80: [00:24:56] WARNING: final character of V3000 array is not ')' -80: [00:24:56] -80: -80: **** -80: Pre-condition Violation -80: bookmark not found -80: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp -80: Failed Expression: (lu != d_bondBookmarks.end()) -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::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::ParseV3000ParseLabel(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_stringstream, std::allocator >&, std::vector, std::allocator >, std::allocator, std::allocator > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) 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# 0x0000556AE9904033 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000556AE997D228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000556AE997DD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000556AE997E1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000556AE994F8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000556AE994FC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000556AE98C2C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x00007F71A3833CA8 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# 0x0000556AE98C2C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: ---------- -80: **** -80: -80: [00:24:56] WARNING: final character of V3000 array is not ')' -80: [00:24:56] -80: -80: **** -80: Pre-condition Violation -80: bookmark not found -80: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp -80: Failed Expression: (lu != d_bondBookmarks.end()) -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::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::ParseV3000ParseLabel(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_stringstream, std::allocator >&, std::vector, std::allocator >, std::allocator, std::allocator > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) 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# 0x0000556AE99040CB in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000556AE997D228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000556AE997DD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000556AE997E1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000556AE994F8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000556AE994FC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000556AE98C2C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x00007F71A3833CA8 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# 0x0000556AE98C2C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: ---------- -80: **** -80: -80: [00:24:56] bookmark not found -80: [00:24:56] SGroup 1 is invalid and will be ignored -80: [00:24:56] WARNING: final character of V3000 array is not ')' -80: [00:24:56] -80: -80: **** -80: Pre-condition Violation -80: bookmark not found -80: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp -80: Failed Expression: (lu != d_atomBookmarks.end()) -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::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::ParseV3000ParseLabel(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_stringstream, std::allocator >&, std::vector, std::allocator >, std::allocator, std::allocator > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) 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# 0x0000556AE9904434 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000556AE997D228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000556AE997DD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000556AE997E1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000556AE994F8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000556AE994FC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000556AE98C2C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x00007F71A3833CA8 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# 0x0000556AE98C2C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: ---------- -80: **** -80: -80: [00:24:56] WARNING: final character of V3000 array is not ')' -80: [00:24:56] -80: -80: **** -80: Pre-condition Violation -80: bookmark not found -80: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp -80: Failed Expression: (lu != d_atomBookmarks.end()) -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::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::ParseV3000ParseLabel(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_stringstream, std::allocator >&, std::vector, std::allocator >, std::allocator, std::allocator > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) 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# 0x0000556AE99044CC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000556AE997D228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000556AE997DD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000556AE997E1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000556AE994F8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000556AE994FC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000556AE98C2C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x00007F71A3833CA8 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# 0x0000556AE98C2C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: ---------- -80: **** -80: -80: [00:24:56] bookmark not found -80: [00:24:56] SGroup 1 is invalid and will be ignored -80: [00:24:56] -80: -80: **** -80: Pre-condition Violation -80: bookmark not found -80: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp -80: Failed Expression: (lu != d_bondBookmarks.end()) -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::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::ParseV3000ParseLabel(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_stringstream, std::allocator >&, std::vector, std::allocator >, std::allocator, std::allocator > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) 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# 0x0000556AE9904833 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000556AE997D228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000556AE997DD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000556AE997E1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000556AE994F8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000556AE994FC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000556AE98C2C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x00007F71A3833CA8 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# 0x0000556AE98C2C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: ---------- -80: **** -80: -80: [00:24:56] -80: -80: **** -80: Pre-condition Violation -80: bookmark not found -80: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp -80: Failed Expression: (lu != d_bondBookmarks.end()) -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::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::ParseV3000ParseLabel(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_stringstream, std::allocator >&, std::vector, std::allocator >, std::allocator, std::allocator > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) 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# 0x0000556AE99048CC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000556AE997D228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000556AE997DD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000556AE997E1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000556AE994F8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000556AE994FC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000556AE98C2C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x00007F71A3833CA8 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# 0x0000556AE98C2C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: ---------- -80: **** -80: -80: [00:24:56] bookmark not found -80: [00:24:56] SGroup 2 is invalid and will be ignored -80: [00:24:56] -80: -80: **** -80: Pre-condition Violation -80: bookmark not found -80: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp -80: Failed Expression: (lu != d_atomBookmarks.end()) -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::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::ParseV3000ParseLabel(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_stringstream, std::allocator >&, std::vector, std::allocator >, std::allocator, std::allocator > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) 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# 0x0000556AE9904C32 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000556AE997D228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000556AE997DD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000556AE997E1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000556AE994F8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000556AE994FC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000556AE98C2C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x00007F71A3833CA8 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# 0x0000556AE98C2C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: ---------- -80: **** -80: -80: [00:24:56] -80: -80: **** -80: Pre-condition Violation -80: bookmark not found -80: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp -80: Failed Expression: (lu != d_atomBookmarks.end()) -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::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::ParseV3000ParseLabel(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_stringstream, std::allocator >&, std::vector, std::allocator >, std::allocator, std::allocator > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) 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# 0x0000556AE9904CCC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000556AE997D228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000556AE997DD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000556AE997E1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000556AE994F8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000556AE994FC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000556AE98C2C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x00007F71A3833CA8 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# 0x0000556AE98C2C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: ---------- -80: **** -80: -80: [00:24:56] bookmark not found -80: [00:24:56] SGroup 2 is invalid and will be ignored -80: [00:24:56] Explicit valence for atom # 2 O, 3, is greater than permitted -80: [00:24:56] Explicit valence for atom # 1 O, 3, is greater than permitted -80: [00:24:56] Explicit valence for atom # 1 C, 5, is greater than permitted -80: [00:24:56] sanitize [00:24:56] UNK: [00:24:56] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -80: [00:24:56] 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: -80: [00:24:56] -80: -80: **** -80: Pre-condition Violation -80: no stream -80: Violation occurred on line 133 in file ./Code/GraphMol/FileParsers/SDMolSupplier.cpp -80: Failed Expression: dp_inStream -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::v2::FileParsers::SDMolSupplier::next() in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 3# 0x0000556AE99393C4 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 4# 0x0000556AE98F4CAD in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 5# 0x0000556AE997D228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 6# 0x0000556AE997DD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 7# 0x0000556AE997E1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x0000556AE994F8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000556AE994FC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000556AE98C2C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x00007F71A3833CA8 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# 0x0000556AE98C2C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: ---------- -80: **** -80: -80: [00:24:56] -80: -80: **** -80: Pre-condition Violation -80: no stream -80: Violation occurred on line 187 in file ./Code/GraphMol/FileParsers/ForwardSDMolSupplier.cpp -80: Failed Expression: dp_inStream -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::v2::FileParsers::ForwardSDMolSupplier::next() in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 3# 0x0000556AE99393C4 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 4# 0x0000556AE98F4E88 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 5# 0x0000556AE997D228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 6# 0x0000556AE997DD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 7# 0x0000556AE997E1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x0000556AE994F8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000556AE994FC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000556AE98C2C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x00007F71A3833CA8 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# 0x0000556AE98C2C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: ---------- -80: **** -80: -80: [00:24:56] -80: -80: **** -81: Randomness seeded to: 1366902074 -81: =============================================================================== -81: All tests passed (95 assertions in 4 test cases) -81: -82: Randomness seeded to: 2738275277 +66: Randomness seeded to: 4067271892 +66: =============================================================================== +66: All tests passed (580 assertions in 18 test cases) +66: +82: Randomness seeded to: 414460452 82: =============================================================================== 82: All tests passed (100 assertions in 2 test cases) 82: -84: Randomness seeded to: 3455441849 -84: [00:24:56] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -84: [00:24:56] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -84: [00:24:56] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -84: [00:24:56] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. + 57/236 Test #82: XYZFileParserCatchTest ................. Passed 0.07 sec +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 +72: [20:24:12] Finished: testMolSup() +72: [20:24:12] ----------------------------------------- +72: +72: [20:24:12] ----------------------------------------- +72: [20:24:12] Finished: testRandMolSup() +72: [20:24:12] ----------------------------------------- +72: +72: [20:24:12] ----------------------------------------- +72: [20:24:12] Finished: testSmilesSup() +72: [20:24:12] ----------------------------------------- +72: +72: [20:24:12] ----------------------------------------- +72: [20:24:12] ------------------------------------------------------ +72: [20:24:12] SMILES Parse Error: syntax error while parsing: fail +72: [20:24:12] SMILES Parse Error: check for mistakes around position 1: +72: [20:24:12] fail +72: [20:24:12] ^ +72: [20:24:12] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' +72: [20:24:12] ERROR: Smiles parse error on line 3 +72: [20:24:12] ERROR: Cannot create molecule from : 'fail' +60: [20:24:12] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +60: [20:24:12] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +60: [20:24:12] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +60: [20:24:12] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +62: [20:24:12] +62: +62: **** +62: Range Error +62: idx +62: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp +62: Failed Expression: 20 < 20 +62: ---------- +62: Stacktrace: +62: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +62: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +62: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +62: 3# RDKit::Canon::canonicalizeFragment(RDKit::ROMol&, int, std::vector >&, std::vector > const&, std::vector >&, boost::dynamic_bitset > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*, bool, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +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# 0x000055A19838CA5D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 8# 0x000055A1983DDD28 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 9# 0x000055A1983DE848 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 10# 0x000055A1983DECC0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 11# 0x000055A1983B0303 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 12# 0x000055A1983B066C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 13# 0x000055A198341E1E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 14# 0x00007FA8A5C33CA8 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# 0x000055A198341E61 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: ---------- +62: **** +62: +62: [20:24:12] SMARTS Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5' +62: [20:24:12] SMILES Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5' +62: [20:24:12] SMARTS Parse Error: syntax error while parsing: C1C)foo +62: [20:24:12] SMARTS Parse Error: Failed parsing SMARTS 'C1C)foo' for input: 'C1C)foo' +62: [20:24:12] SMILES Parse Error: extra close parentheses while parsing: C1C)foo +62: [20:24:12] SMILES Parse Error: check for mistakes around position 4: +62: [20:24:12] C1C)foo +62: [20:24:12] ~~~^ +62: [20:24:12] SMILES Parse Error: Failed parsing SMILES 'C1C)foo' for input: 'C1C)foo' +62: =============================================================================== +62: All tests passed (1588 assertions in 69 test cases) +62: +70: [20:24:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [20:24:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [20:24:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [20:24:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [20:24:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [20:24:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [20:24:12] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +70: [20:24:12] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +70: [20:24:12] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +70: [20:24:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [20:24:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [20:24:12] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +70: [20:24:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [20:24:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [20:24:12] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +70: [20:24:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [20:24:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [20:24:12] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +70: [20:24:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [20:24:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [20:24:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [20:24:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [20:24:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [20:24:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [20:24:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [20:24:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [20:24:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [20:24:12] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +70: [20:24:12] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +70: [20:24:12] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +70: [20:24:12] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +70: [20:24:12] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +70: [20:24:12] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +70: [20:24:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [20:24:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [20:24:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [20:24:12] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +70: [20:24:12] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +70: [20:24:12] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +70: [20:24:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [20:24:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [20:24:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [20:24:12] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +70: [20:24:12] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +70: [20:24:12] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +46: [20:24:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +46: [20:24:12] Explicit valence for atom # 0 Al, 6, is greater than permitted +46: [20:24:12] Explicit valence for atom # 0 Al, 6, is greater than permitted +46: [20:24:12] Explicit valence for atom # 1 Si, 6, is greater than permitted +46: [20:24:12] Explicit valence for atom # 1 Si, 6, is greater than permitted +46: [20:24:12] Explicit valence for atom # 0 P, 6, is greater than permitted +46: [20:24:12] Explicit valence for atom # 0 P, 6, is greater than permitted +46: [20:24:12] Explicit valence for atom # 0 P, 7, is greater than permitted +46: [20:24:12] Explicit valence for atom # 0 P, 7, is greater than permitted +46: [20:24:12] Explicit valence for atom # 1 As, 6, is greater than permitted +46: [20:24:12] Explicit valence for atom # 1 As, 6, is greater than permitted +46: [20:24:12] Explicit valence for atom # 1 As, 7, is greater than permitted +46: [20:24:12] Explicit valence for atom # 1 As, 7, is greater than permitted +46: [20:24:12] Explicit valence for atom # 0 Sb, 6, is greater than permitted +46: [20:24:12] Explicit valence for atom # 0 Sb, 6, is greater than permitted +46: [20:24:12] Explicit valence for atom # 0 Sb, 7, is greater than permitted +46: [20:24:12] Explicit valence for atom # 0 Sb, 7, is greater than permitted +46: [20:24:12] Explicit valence for atom # 1 Bi, 6, is greater than permitted +46: [20:24:12] Explicit valence for atom # 1 Bi, 6, is greater than permitted +46: [20:24:12] Explicit valence for atom # 1 Bi, 8, is greater than permitted +46: [20:24:12] Explicit valence for atom # 1 Bi, 8, is greater than permitted +46: =============================================================================== +46: All tests passed (4479 assertions in 107 test cases) +46: +84: Randomness seeded to: 1553893048 +84: [20:24:12] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +84: [20:24:12] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +84: [20:24:12] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +84: [20:24:12] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. 84: =============================================================================== 84: All tests passed (142 assertions in 6 test cases) 84: -85: Randomness seeded to: 3360159992 +85: Randomness seeded to: 2165077748 85: =============================================================================== 85: All tests passed (8 assertions in 1 test case) 85: -86: Randomness seeded to: 391236021 -86: [00:24:56] Ignoring invalid chirality label: '12_R_1_3_4_5' -86: [00:24:56] Ignoring invalid chirality label: '12_ANR_1_3_4_15' -86: [00:24:56] Ignoring invalid chirality label: '2_S_1_3_4' -86: [00:24:56] Ignoring invalid chirality label: '2_ANS_1_3_4_5_2' +30: ...[20:24:12] Molecule does not have explicit Hs. Consider calling AddHs() +73: [20:24:12] Finished: testMae() +73: [20:24:12] ----------------------------------------- +73: +73: [20:24:12] +73: ----------------------------------------- +73: [20:24:12] Finished: testTdt() +73: [20:24:12] ----------------------------------------- +73: +83: Randomness seeded to: 2658041358 +83: [20:24:12] Invalid or missing fragment id from CDXML fragment, assigning new one... +83: [20:24:12] Explicit valence for atom # 3 N, 4, is greater than permitted +83: [20:24:12] CDXMLParser: failed sanitizing skipping fragment 32 +83: [20:24:12] Bad bond in CDXML skipping fragment 58... +83: [20:24:12] Invalid or missing fragment id from CDXML fragment, assigning new one... +83: [20:24:12] Bad bond in CDXML skipping fragment 58... +83: [20:24:12] WARNING: not removing hydrogen atom without neighbors +83: [20:24:12] WARNING: not removing hydrogen atom without neighbors +83: [20:24:12] WARNING: not removing hydrogen atom without neighbors +83: [20:24:12] WARNING: not removing hydrogen atom without neighbors +83: [20:24:12] WARNING: not removing hydrogen atom without neighbors +83: [20:24:12] WARNING: not removing hydrogen atom without neighbors +83: [20:24:12] WARNING: not removing hydrogen atom without neighbors +83: [20:24:12] WARNING: not removing hydrogen atom without neighbors +83: [20:24:12] WARNING: not removing hydrogen atom without neighbors +83: [20:24:12] WARNING: not removing hydrogen atom without neighbors +83: [20:24:12] CDXMLParser: Schema 80180 step 80181 ReactionStepAgents reaction fragment 64603 not found in document. +86: Randomness seeded to: 3597489910 +86: [20:24:12] Ignoring invalid chirality label: '12_R_1_3_4_5' +86: [20:24:12] Ignoring invalid chirality label: '12_ANR_1_3_4_15' +86: [20:24:12] Ignoring invalid chirality label: '2_S_1_3_4' +86: [20:24:12] Ignoring invalid chirality label: '2_ANS_1_3_4_5_2' 86: =============================================================================== 86: All tests passed (24 assertions in 6 test cases) 86: -87: Randomness seeded to: 231677023 +87: Randomness seeded to: 2017876962 87: =============================================================================== 87: All tests passed (6 assertions in 1 test case) 87: -88: Randomness seeded to: 2001316473 -88: =============================================================================== -88: All tests passed (26 assertions in 2 test cases) -88: -90: ----------------- Test 1 -90: Done -90: -90: ----------------- Test 2 -90: Done -90: -90: ----------------- Test 3 -90: Done -90: -90: ----------------- Test 4 -90: Done -90: -90: ----------------- Test 5 -90: Done -90: -90: ----------------- Test 5 QueryRoot -90: Done -90: -90: ----------------- Test 6 (Issue71 related) -90: Done -90: -90: ----------------- Testing serial numbers on recursive queries -90: Done -90: -90: [00:24:56] ------------------------------------- -90: [00:24:56] Test multithreading -90: reading molecules -90: hits: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 -90: processing -90: launch :0 -90: launch :1 -90: launch :2 -90: launch :3 - 58/236 Test #73: testGeneralFileReader .................. Passed 0.15 sec - 59/236 Test #76: testTplParser .......................... Passed 0.13 sec - 60/236 Test #77: testMol2ToMol .......................... Passed 0.13 sec - 61/236 Test #78: testSequence ........................... Passed 0.12 sec - 62/236 Test #79: testExtendedStereoParsing .............. Passed 0.12 sec - 63/236 Test #81: testPropertyLists ...................... Passed 0.11 sec - 64/236 Test #82: XYZFileParserCatchTest ................. Passed 0.08 sec - 65/236 Test #84: molfileStereoCatchTest ................. Passed 0.08 sec - 66/236 Test #85: connectTheDotsTest ..................... Passed 0.07 sec - 67/236 Test #86: v2MolSuppliers ......................... Passed 0.07 sec - 68/236 Test #87: v2FileParsersCatchTest ................. Passed 0.07 sec - 69/236 Test #88: atropisomersCatch ...................... Passed 0.07 sec + 58/236 Test #21: testPyGeometry ......................... Passed 0.35 sec + 59/236 Test #46: graphmolTestsCatch ..................... Passed 0.29 sec + 60/236 Test #58: smiTest1 ............................... Passed 0.25 sec + 61/236 Test #62: smiTestCatch ........................... Passed 0.23 sec + 62/236 Test #66: depictorCatch .......................... Passed 0.21 sec + 63/236 Test #73: testGeneralFileReader .................. Passed 0.16 sec + 64/236 Test #78: testSequence ........................... Passed 0.12 sec + 65/236 Test #84: molfileStereoCatchTest ................. Passed 0.10 sec + 66/236 Test #85: connectTheDotsTest ..................... Passed 0.09 sec + 67/236 Test #86: v2MolSuppliers ......................... Passed 0.08 sec + 68/236 Test #87: v2FileParsersCatchTest ................. Passed 0.08 sec +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 @@ -20188,69 +20099,288 @@ 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 -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 -test 111 - Start 111: testDescriptors - -111: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testDescriptors -111: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -111: Test timeout computed to be: 1500 -60: [00:24:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -60: [00:24:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -60: [00:24:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -60: [00:24:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +72: [20:24:12] ------------------------------------------------------ +72: [20:24:12] ------------------------------------------------------ +72: [20:24:12] >>> This may result in an infinite loop. It should finish almost immediately: +72: [20:24:12] <<< done. +72: [20:24:12] Finished: testSmilesSupFromText() +72: [20:24:12] ----------------------------------------- +72: +72: [20:24:12] ----------------------------------------- +72: [20:24:12] Finished: testSmilesWriter() +72: [20:24:12] ----------------------------------------- +72: +72: [20:24:12] ----------------------------------------- +72: [20:24:12] Finished: testSDWriter() +72: [20:24:12] ----------------------------------------- +72: +72: [20:24:12] ----------------------------------------- +72: [20:24:12] Finished: testSDSupplierEnding() +72: [20:24:12] ----------------------------------------- +72: +72: [20:24:12] ----------------------------------------- +72: [20:24:12] Finished: testSuppliersEmptyFile() +72: [20:24:12] ----------------------------------------- +72: +72: [20:24:12] ----------------------------------------- +72: [20:24:12] Finished: testCisTrans() +72: [20:24:12] ----------------------------------------- +72: +72: [20:24:12] ----------------------------------------- +72: [20:24:12] Finished: testStereoRound() +72: [20:24:12] ----------------------------------------- +72: +72: [20:24:12] ----------------------------------------- +72: [20:24:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +72: [20:24:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +72: [20:24:12] Finished: testIssue226() +72: [20:24:12] ----------------------------------------- +72: +72: [20:24:12] ----------------------------------------- +72: [20:24:12] Finished: testTDTSupplier1() +72: [20:24:12] ----------------------------------------- +72: +72: [20:24:12] ----------------------------------------- +72: [20:24:12] Finished: testTDTSupplier2() +72: [20:24:12] ----------------------------------------- +72: +72: [20:24:12] ----------------------------------------- +72: [20:24:12] Finished: testTDTSupplier3() +72: [20:24:12] ----------------------------------------- +72: +72: [20:24:12] ----------------------------------------- +72: [20:24:12] Finished: testSDSupplierFromText() +72: [20:24:12] ----------------------------------------- +72: +72: [20:24:12] ----------------------------------------- +72: [20:24:12] ERROR: Problems encountered parsing data fields +72: [20:24:12] ERROR: moving to the beginning of the next molecule +72: [20:24:12] ERROR: Problems encountered parsing data fields +72: [20:24:12] ERROR: moving to the beginning of the next molecule +72: [20:24:12] Spurious data before the first property will be ignored +72: [20:24:12] Property will be truncated after the first blank line +72: [20:24:12] Property will be truncated after the first blank line +72: [20:24:12] Property will be truncated after the first blank line +72: [20:24:12] Finished: testSDSupplierStrLax1() +72: [20:24:12] ----------------------------------------- +72: +72: [20:24:12] ----------------------------------------- +72: [20:24:12] ERROR: Problems encountered parsing data fields +72: [20:24:12] ERROR: moving to the beginning of the next molecule +72: [20:24:12] Property will be truncated after the first blank line +72: [20:24:12] Finished: testSDSupplierStrLax2() +72: [20:24:12] ----------------------------------------- +72: +72: [20:24:12] ----------------------------------------- +72: [20:24:12] ERROR: Problems encountered parsing data fields +72: [20:24:12] ERROR: moving to the beginning of the next molecule +72: [20:24:12] ERROR: Problems encountered parsing data fields +72: [20:24:12] ERROR: moving to the beginning of the next molecule +72: [20:24:12] Spurious data before the first property will be ignored +72: [20:24:12] Property will be truncated after the first blank line +72: [20:24:12] Property will be truncated after the first blank line +72: [20:24:12] Property will be truncated after the first blank line +72: [20:24:12] Finished: testSDSupplierFromTextStrLax1() +72: [20:24:12] ----------------------------------------- +72: +72: [20:24:12] ----------------------------------------- +72: [20:24:12] ERROR: Problems encountered parsing data fields +72: [20:24:12] ERROR: moving to the beginning of the next molecule +72: [20:24:12] Property will be truncated after the first blank line +72: [20:24:12] Finished: testSDSupplierFromTextStrLax2() +72: [20:24:12] ----------------------------------------- +72: +72: [20:24:12] ----------------------------------------- +72: [20:24:12] Finished: testIssue265() +72: [20:24:12] ----------------------------------------- +72: +72: [20:24:12] ----------------------------------------- +72: [20:24:12] ERROR: End of data field name not found +72: [20:24:12] ERROR: moving to the beginning of the next molecule +72: [20:24:12] Explicit valence for atom # 0 F, 2, is greater than permitted +72: [20:24:12] ERROR: Could not sanitize molecule ending on line 16 +72: [20:24:12] ERROR: Explicit valence for atom # 0 F, 2, is greater than permitted +72: [20:24:12] ERROR: Atom line too short: ' 1 2 1 0 0 0 0' on line 12 +72: [20:24:12] ERROR: moving to the beginning of the next molecule +72: [20:24:12] ERROR: Bond line too short: 'M END' on line 18 +72: [20:24:12] ERROR: moving to the beginning of the next molecule +72: [20:24:12] Finished: testSDErrorHandling() +72: [20:24:12] ----------------------------------------- +72: +72: [20:24:12] ----------------------------------------- +72: [20:24:12] Finished: testIssue381() +72: [20:24:12] ----------------------------------------- +72: +72: [20:24:12] ----------------------------------------- +72: [20:24:12] Finished: testSetStreamIndices() +72: [20:24:12] ----------------------------------------- +72: +72: [20:24:12] ----------------------------------------- +72: [20:24:12] Finished: testMixIterAndRandom() +72: [20:24:12] ----------------------------------------- +72: +72: [20:24:12] ----------------------------------------- +72: build: +72: [20:24:12] Finished: testRemoveHs() +72: [20:24:12] ----------------------------------------- +72: +72: [20:24:12] ----------------------------------------- +72: [20:24:12] Finished: testGetItemText() +72: [20:24:12] ----------------------------------------- +72: +72: [20:24:12] ----------------------------------------- +72: [20:24:12] Finished: testForwardSDSupplier() +72: [20:24:12] ----------------------------------------- +72: +72: [20:24:12] ----------------------------------------- +72: [20:24:12] Finished: testMissingCRSDSupplier() +72: [20:24:12] ----------------------------------------- +72: +72: [20:24:12] ----------------------------------------- +72: [20:24:12] Finished: testIssue3482695() +72: [20:24:12] ----------------------------------------- +72: +72: [20:24:12] ----------------------------------------- 60: Test 60: -60: RP-6306_atropBad2.cxsmi +60: JDQ443_3d.cxsmi 60: -60: [00:24:56] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -60: [00:24:56] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -60: [00:24:56] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -60: [00:24:56] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -60: [00:24:56] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 60: Test 60: -60: RP-6306_3d.cxsmi +60: JDQ443_atrop1.cxsmi 60: 60: Test 60: -60: Sotorasib_atrop1.cxsmi +60: JDQ443_atrop2.cxsmi 60: 60: Test 60: -60: Sotorasib_atrop2.cxsmi +60: JDQ443_atrop3.cxsmi 60: 60: Test 60: -60: Sotorasib_atrop3.cxsmi +60: JDQ443_atrop4.cxsmi 60: 60: Test 60: -60: Sotorasib_atrop4.cxsmi +60: JDQ443_atropBad1.cxsmi 60: +60: [20:24:12] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +60: [20:24:12] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +60: [20:24:12] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +60: [20:24:12] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +60: [20:24:12] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 60: Test 60: -60: Sotorasib_atrop5.cxsmi +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: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: RP-6306_atrop4.cxsmi +60: +60: Test +60: +60: RP-6306_atrop5.cxsmi +60: +60: [20:24:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [20:24:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [20:24:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [20:24:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [20:24:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [20:24:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [20:24:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [20:24:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [20:24:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [20:24:12] 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: [20:24:12] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +60: [20:24:12] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +60: [20:24:12] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +60: [20:24:12] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +60: [20:24:12] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +60: Test +60: +60: RP-6306_atropBad2.cxsmi +60: +60: [20:24:12] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +60: [20:24:12] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +60: [20:24:12] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +60: [20:24:12] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +60: [20:24:12] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +80: [20:24:12] 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: +80: [20:24:12] +80: +80: **** +80: Pre-condition Violation +80: no stream +80: Violation occurred on line 133 in file ./Code/GraphMol/FileParsers/SDMolSupplier.cpp +80: Failed Expression: dp_inStream +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::v2::FileParsers::SDMolSupplier::next() in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 3# 0x0000556E855123C4 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 4# 0x0000556E854CDCAD in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 5# 0x0000556E85556228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 6# 0x0000556E85556D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 7# 0x0000556E855571C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x0000556E855288C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000556E85528C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000556E8549BC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x00007FC76AC33CA8 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# 0x0000556E8549BC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: ---------- +80: **** +80: +80: [20:24:12] +80: +80: **** +80: Pre-condition Violation +80: no stream +80: Violation occurred on line 187 in file ./Code/GraphMol/FileParsers/ForwardSDMolSupplier.cpp +80: Failed Expression: dp_inStream +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::v2::FileParsers::ForwardSDMolSupplier::next() in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 3# 0x0000556E855123C4 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 4# 0x0000556E854CDE88 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 5# 0x0000556E85556228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 6# 0x0000556E85556D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 7# 0x0000556E855571C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x0000556E855288C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000556E85528C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000556E8549BC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x00007FC76AC33CA8 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# 0x0000556E8549BC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: ---------- +80: **** +80: +80: [20:24:12] +80: +80: **** 80: Pre-condition Violation 80: no stream 80: Violation occurred on line 409 in file ./Code/GraphMol/FileParsers/SmilesMolSupplier.cpp @@ -20260,21 +20390,21 @@ 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# 0x0000556AE99393C4 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 4# 0x0000556AE98F52C1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 5# 0x0000556AE997D228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 6# 0x0000556AE997DD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 7# 0x0000556AE997E1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x0000556AE994F8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000556AE994FC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000556AE98C2C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x00007F71A3833CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 3# 0x0000556E855123C4 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 4# 0x0000556E854CE2C1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 5# 0x0000556E85556228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 6# 0x0000556E85556D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 7# 0x0000556E855571C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x0000556E855288C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000556E85528C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000556E8549BC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x00007FC76AC33CA8 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# 0x0000556AE98C2C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000556E8549BC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [00:24:56] +80: [20:24:12] 80: 80: **** 80: Pre-condition Violation @@ -20286,21 +20416,21 @@ 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# 0x0000556AE99393C4 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 4# 0x0000556AE98F5646 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 5# 0x0000556AE997D228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 6# 0x0000556AE997DD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 7# 0x0000556AE997E1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x0000556AE994F8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000556AE994FC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000556AE98C2C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x00007F71A3833CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 3# 0x0000556E855123C4 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 4# 0x0000556E854CE646 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 5# 0x0000556E85556228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 6# 0x0000556E85556D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 7# 0x0000556E855571C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x0000556E855288C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000556E85528C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000556E8549BC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x00007FC76AC33CA8 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# 0x0000556AE98C2C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000556E8549BC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [00:24:56] +80: [20:24:12] 80: 80: **** 80: Pre-condition Violation @@ -20312,29 +20442,29 @@ 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# 0x0000556AE99393C4 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 4# 0x0000556AE98F58C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 5# 0x0000556AE997D228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 6# 0x0000556AE997DD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 7# 0x0000556AE997E1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x0000556AE994F8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000556AE994FC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000556AE98C2C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x00007F71A3833CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 3# 0x0000556E855123C4 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 4# 0x0000556E854CE8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 5# 0x0000556E85556228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 6# 0x0000556E85556D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 7# 0x0000556E855571C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x0000556E855288C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000556E85528C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000556E8549BC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x00007FC76AC33CA8 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# 0x0000556AE98C2C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000556E8549BC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [00:24:56] Found a SCD/SED line with missing/empty SDT specification at line 21 -80: [00:24:56] Found a SCD/SED line with missing/empty SDT specification at line 20 -80: [00:24:56] BEGIN SGROUP line not found on line 14 -80: [00:24:56] Unhandled CTAB feature: 'Unsupported SGroup type '' on line 18'. Molecule skipped. -80: [00:24:56] END SGROUP line not found on line 14 -80: [00:24:56] END SGROUP line not found on line 14 -80: [00:24:56] MRV_COORDINATE_BOND_TYPE SGroup with value 0 does not reference a query bond, ignoring. -80: [00:24:56] MRV_COORDINATE_BOND_TYPE SGroup with value 1 does not reference a query bond, ignoring. -80: [00:24:56] +80: [20:24:12] Found a SCD/SED line with missing/empty SDT specification at line 21 +80: [20:24:12] Found a SCD/SED line with missing/empty SDT specification at line 20 +80: [20:24:12] BEGIN SGROUP line not found on line 14 +80: [20:24:12] Unhandled CTAB feature: 'Unsupported SGroup type '' on line 18'. Molecule skipped. +80: [20:24:12] END SGROUP line not found on line 14 +80: [20:24:12] END SGROUP line not found on line 14 +80: [20:24:12] MRV_COORDINATE_BOND_TYPE SGroup with value 0 does not reference a query bond, ignoring. +80: [20:24:12] MRV_COORDINATE_BOND_TYPE SGroup with value 1 does not reference a query bond, ignoring. +80: [20:24:12] 80: 80: **** 80: Range Error @@ -20349,38 +20479,38 @@ 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# 0x0000556AE9938FDF in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 7# 0x0000556AE98FACC3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x0000556AE997D228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000556AE997DD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000556AE997E1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000556AE994F8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000556AE994FC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000556AE98C2C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x00007F71A3833CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 6# 0x0000556E85511FDF in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 7# 0x0000556E854D3CC3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x0000556E85556228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000556E85556D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000556E855571C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000556E855288C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000556E85528C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000556E8549BC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x00007FC76AC33CA8 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# 0x0000556AE98C2C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x0000556E8549BC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [00:24:56] molecule does not contain a bond matching the MRV_COORDINATE_BOND_TYPE SGroup for bond 99, ignoring. -80: [00:24:56] Multiple ATTCHPT values for atom 2 on line 9 -80: [00:24:56] Found a SCD/SED line with missing/empty SDT specification at line 12 -80: [00:24:56] SMARTS Parse Error: syntax error while parsing: [#6;R -80: [00:24:56] SMARTS Parse Error: Failed parsing SMARTS '[#6;R' for input: '[#6;R' -80: [00:24:56] SMARTS for SMARTSQ '[#6;R' could not be parsed or has no atoms. Ignoring it. -80: [00:24:56] Skipping empty SMARTS value for SMARTSQ. -80: [00:24:56] unrecognized QUERYOP '>' for SMARTSQ. Query ignored. -80: [00:24:56] Found a SCD/SED line with missing/empty SDT specification at line 12 -80: [00:24:56] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -80: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -80: [00:24:56] WARNING: Skipping property bar because the value includes an illegal blank line -80: [00:24:56] WARNING: Skipping property baz because the value includes an illegal blank line -80: [00:24:56] WARNING: Skipping property bletch +80: [20:24:12] molecule does not contain a bond matching the MRV_COORDINATE_BOND_TYPE SGroup for bond 99, ignoring. +80: [20:24:12] Multiple ATTCHPT values for atom 2 on line 9 +80: [20:24:12] Found a SCD/SED line with missing/empty SDT specification at line 12 +80: [20:24:12] SMARTS Parse Error: syntax error while parsing: [#6;R +80: [20:24:12] SMARTS Parse Error: Failed parsing SMARTS '[#6;R' for input: '[#6;R' +80: [20:24:12] SMARTS for SMARTSQ '[#6;R' could not be parsed or has no atoms. Ignoring it. +80: [20:24:12] Skipping empty SMARTS value for SMARTSQ. +80: [20:24:12] unrecognized QUERYOP '>' for SMARTSQ. Query ignored. +80: [20:24:12] Found a SCD/SED line with missing/empty SDT specification at line 12 +80: [20:24:12] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +80: [20:24:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +80: [20:24:12] WARNING: Skipping property bar because the value includes an illegal blank line +80: [20:24:12] WARNING: Skipping property baz because the value includes an illegal blank line +80: [20:24:12] WARNING: Skipping property bletch 80: nope because the name includes a newline -80: [00:24:56] WARNING: Skipping property bletch +80: [20:24:12] WARNING: Skipping property bletch 80: nope2 because the name includes a newline -80: [00:24:56] +80: [20:24:12] 80: 80: **** 80: Post-condition Violation @@ -20392,26 +20522,26 @@ 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# 0x00007F71A42C8531 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 4# 0x00007F71A42D3AC2 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# 0x00007F71A42D4FAD in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 3# 0x00007FC76B6C8531 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 4# 0x00007FC76B6D3AC2 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x00007FC76B6D4FAD 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# 0x0000556AE98CC35C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000556AE997D228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000556AE997DD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000556AE997E1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000556AE994F8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000556AE994FC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000556AE98C2C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x00007F71A3833CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 9# 0x0000556E854A535C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000556E85556228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000556E85556D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000556E855571C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000556E855288C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000556E85528C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000556E8549BC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x00007FC76AC33CA8 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# 0x0000556AE98C2C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000556E8549BC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [00:24:56] +80: [20:24:12] 80: 80: **** 80: Post-condition Violation @@ -20423,26 +20553,26 @@ 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# 0x00007F71A42C8531 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 4# 0x00007F71A42D3AC2 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# 0x00007F71A42D4FAD in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 3# 0x00007FC76B6C8531 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 4# 0x00007FC76B6D3AC2 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x00007FC76B6D4FAD 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# 0x0000556AE98CBA3A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000556AE997D228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000556AE997DD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000556AE997E1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000556AE994F8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000556AE994FC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000556AE98C2C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x00007F71A3833CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 9# 0x0000556E854A4A3A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000556E85556228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000556E85556D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000556E855571C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000556E855288C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000556E85528C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000556E8549BC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x00007FC76AC33CA8 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# 0x0000556AE98C2C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000556E8549BC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [00:24:56] +80: [20:24:12] 80: 80: **** 80: Post-condition Violation @@ -20454,26 +20584,26 @@ 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# 0x00007F71A42C8531 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 4# 0x00007F71A42D1DFA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# 0x00007F71A42D217D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 3# 0x00007FC76B6C8531 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 4# 0x00007FC76B6D1DFA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x00007FC76B6D217D 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# 0x0000556AE98CC304 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000556AE997D228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000556AE997DD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000556AE997E1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000556AE994F8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000556AE994FC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000556AE98C2C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x00007F71A3833CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 9# 0x0000556E854A5304 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000556E85556228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000556E85556D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000556E855571C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000556E855288C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000556E85528C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000556E8549BC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x00007FC76AC33CA8 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# 0x0000556AE98C2C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000556E8549BC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [00:24:56] +80: [20:24:12] 80: 80: **** 80: Post-condition Violation @@ -20485,28 +20615,28 @@ 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# 0x00007F71A42C8531 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 4# 0x00007F71A42D1DFA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# 0x00007F71A42D217D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 3# 0x00007FC76B6C8531 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 4# 0x00007FC76B6D1DFA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x00007FC76B6D217D 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# 0x0000556AE98CBFA2 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000556AE997D228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000556AE997DD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000556AE997E1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000556AE994F8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000556AE994FC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000556AE98C2C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x00007F71A3833CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 9# 0x0000556E854A4FA2 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000556E85556228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000556E85556D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000556E855571C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000556E855288C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000556E85528C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000556E8549BC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x00007FC76AC33CA8 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# 0x0000556AE98C2C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000556E8549BC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [00:24:56] atom 3 has a negative isotope value. line: 15 -80: [00:24:56] Ignoring invalid chirality label: '2_bad_chirality' -80: [00:24:56] +80: [20:24:12] atom 3 has a negative isotope value. line: 15 +80: [20:24:12] Ignoring invalid chirality label: '2_bad_chirality' +80: [20:24:12] 80: 80: **** 80: Pre-condition Violation @@ -20519,655 +20649,327 @@ 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# 0x0000556AE990E7A5 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 5# 0x0000556AE997D228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 6# 0x0000556AE997DD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 7# 0x0000556AE997E1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x0000556AE994F8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000556AE994FC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000556AE98C2C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x00007F71A3833CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 4# 0x0000556E854E77A5 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 5# 0x0000556E85556228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 6# 0x0000556E85556D48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 7# 0x0000556E855571C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x0000556E855288C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000556E85528C2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000556E8549BC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x00007FC76AC33CA8 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# 0x0000556AE98C2C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000556E8549BC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -72: [00:24:56] Finished: testMolSup() -72: [00:24:56] ----------------------------------------- -72: -72: [00:24:56] ----------------------------------------- -72: [00:24:56] Finished: testRandMolSup() -72: [00:24:56] ----------------------------------------- -72: -72: [00:24:56] ----------------------------------------- -72: [00:24:56] Finished: testSmilesSup() -72: [00:24:56] ----------------------------------------- -72: -72: [00:24:56] ----------------------------------------- -72: [00:24:56] ------------------------------------------------------ -72: [00:24:56] SMILES Parse Error: syntax error while parsing: fail -72: [00:24:56] SMILES Parse Error: check for mistakes around position 1: -72: [00:24:56] fail -72: [00:24:56] ^ -72: [00:24:56] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' -72: [00:24:56] ERROR: Smiles parse error on line 3 -72: [00:24:56] ERROR: Cannot create molecule from : 'fail' -72: [00:24:56] ------------------------------------------------------ -72: [00:24:56] ------------------------------------------------------ -72: [00:24:56] >>> This may result in an infinite loop. It should finish almost immediately: -72: [00:24:56] <<< done. -72: [00:24:56] Finished: testSmilesSupFromText() -72: [00:24:56] ----------------------------------------- -72: -72: [00:24:56] ----------------------------------------- -72: [00:24:56] Finished: testSmilesWriter() -72: [00:24:56] ----------------------------------------- -72: -72: [00:24:56] ----------------------------------------- -72: [00:24:56] Finished: testSDWriter() -72: [00:24:56] ----------------------------------------- -72: -72: [00:24:56] ----------------------------------------- -72: [00:24:56] Finished: testSDSupplierEnding() -72: [00:24:56] ----------------------------------------- -72: -72: [00:24:56] ----------------------------------------- -72: [00:24:56] Finished: testSuppliersEmptyFile() -72: [00:24:56] ----------------------------------------- -72: -72: [00:24:56] ----------------------------------------- -72: [00:24:56] Finished: testCisTrans() -72: [00:24:56] ----------------------------------------- -72: -72: [00:24:56] ----------------------------------------- -72: [00:24:56] Finished: testStereoRound() -72: [00:24:56] ----------------------------------------- -72: -72: [00:24:56] ----------------------------------------- -72: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -72: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -72: [00:24:56] Finished: testIssue226() -72: [00:24:56] ----------------------------------------- -72: -72: [00:24:56] ----------------------------------------- -72: [00:24:56] Finished: testTDTSupplier1() -72: [00:24:56] ----------------------------------------- -72: -72: [00:24:56] ----------------------------------------- -72: [00:24:56] Finished: testTDTSupplier2() -72: [00:24:56] ----------------------------------------- -72: -72: [00:24:56] ----------------------------------------- -72: [00:24:56] Finished: testTDTSupplier3() -72: [00:24:56] ----------------------------------------- -72: -72: [00:24:56] ----------------------------------------- -72: [00:24:56] Finished: testSDSupplierFromText() -72: [00:24:56] ----------------------------------------- -72: -72: [00:24:56] ----------------------------------------- -72: [00:24:56] ERROR: Problems encountered parsing data fields -72: [00:24:56] ERROR: moving to the beginning of the next molecule -72: [00:24:56] ERROR: Problems encountered parsing data fields -72: [00:24:56] ERROR: moving to the beginning of the next molecule -72: [00:24:56] Spurious data before the first property will be ignored -72: [00:24:56] Property will be truncated after the first blank line -72: [00:24:56] Property will be truncated after the first blank line -72: [00:24:56] Property will be truncated after the first blank line -72: [00:24:56] Finished: testSDSupplierStrLax1() -72: [00:24:56] ----------------------------------------- -72: -72: [00:24:56] ----------------------------------------- -72: [00:24:56] ERROR: Problems encountered parsing data fields -72: [00:24:56] ERROR: moving to the beginning of the next molecule -72: [00:24:56] Property will be truncated after the first blank line -72: [00:24:56] Finished: testSDSupplierStrLax2() -72: [00:24:56] ----------------------------------------- -72: -72: [00:24:56] ----------------------------------------- -72: [00:24:56] ERROR: Problems encountered parsing data fields -72: [00:24:56] ERROR: moving to the beginning of the next molecule -72: [00:24:56] ERROR: Problems encountered parsing data fields -72: [00:24:56] ERROR: moving to the beginning of the next molecule -72: [00:24:56] Spurious data before the first property will be ignored -72: [00:24:56] Property will be truncated after the first blank line -72: [00:24:56] Property will be truncated after the first blank line -72: [00:24:56] Property will be truncated after the first blank line -72: [00:24:56] Finished: testSDSupplierFromTextStrLax1() -72: [00:24:56] ----------------------------------------- -72: -72: [00:24:56] ----------------------------------------- -72: [00:24:56] ERROR: Problems encountered parsing data fields -72: [00:24:56] ERROR: moving to the beginning of the next molecule -72: [00:24:56] Property will be truncated after the first blank line -72: [00:24:56] Finished: testSDSupplierFromTextStrLax2() -72: [00:24:56] ----------------------------------------- -72: -72: [00:24:56] ----------------------------------------- -72: [00:24:56] Finished: testIssue265() -72: [00:24:56] ----------------------------------------- -72: -72: [00:24:56] ----------------------------------------- -72: [00:24:56] ERROR: End of data field name not found -72: [00:24:56] ERROR: moving to the beginning of the next molecule -72: [00:24:56] Explicit valence for atom # 0 F, 2, is greater than permitted -72: [00:24:56] ERROR: Could not sanitize molecule ending on line 16 -72: [00:24:56] ERROR: Explicit valence for atom # 0 F, 2, is greater than permitted -72: [00:24:56] ERROR: Atom line too short: ' 1 2 1 0 0 0 0' on line 12 -72: [00:24:56] ERROR: moving to the beginning of the next molecule -72: [00:24:56] ERROR: Bond line too short: 'M END' on line 18 -72: [00:24:56] ERROR: moving to the beginning of the next molecule -72: [00:24:56] Finished: testSDErrorHandling() -72: [00:24:56] ----------------------------------------- -72: -72: [00:24:56] ----------------------------------------- -72: [00:24:56] Finished: testIssue381() -72: [00:24:56] ----------------------------------------- -72: -72: [00:24:56] ----------------------------------------- -72: [00:24:56] Finished: testSetStreamIndices() -72: [00:24:56] ----------------------------------------- -72: -72: [00:24:56] ----------------------------------------- -72: [00:24:56] Finished: testMixIterAndRandom() -72: [00:24:56] ----------------------------------------- -72: -72: [00:24:56] ----------------------------------------- -72: build: -72: [00:24:56] Finished: testRemoveHs() -72: [00:24:56] ----------------------------------------- -72: -72: [00:24:56] ----------------------------------------- -94: [00:24:56] ------------------------------------- -94: [00:24:56] Test Reaction StructuralFingerprint -94: [00:24:56] ------------------------------------- -94: [00:24:56] Test Reaction DifferenceFingerprint - 70/236 Test #94: testReactionFingerprints ............... Passed 0.17 sec -70: [00:24:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -70: [00:24:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -70: [00:24:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +80: [20:24:12] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +80: [20:24:12] 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.[20:24:12] 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: [20:24:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +80: [20:24:12] 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: [20:24:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +88: Randomness seeded to: 84214303 +88: =============================================================================== +88: All tests passed (26 assertions in 2 test cases) +88: + 69/236 Test #88: atropisomersCatch ...................... Passed 0.15 sec +40: [20:24:12] sorting (hanoi sort) vectors +90: ----------------- Test 1 +90: Done +90: +90: ----------------- Test 2 +90: Done +90: +90: ----------------- Test 3 +90: Done +90: +90: ----------------- Test 4 +90: Done +90: +90: ----------------- Test 5 +90: Done +90: +90: ----------------- Test 5 QueryRoot +90: Done +90: +90: ----------------- Test 6 (Issue71 related) +90: Done +90: +90: ----------------- Testing serial numbers on recursive queries +90: Done +90: +90: [20:24:12] ------------------------------------- +90: [20:24:12] Test multithreading +90: reading molecules +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: [00:24:56] SMARTS Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] -93: [00:24:56] SMARTS Parse Error: Failed parsing SMARTS '[Q:1][C:2][C:3](=[O:4])[O:5]' for input: '[Q:1][C:2][C:3](=[O:4])[O:5]' +93: [20:24:12] SMARTS Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] +93: [20:24:12] SMARTS Parse Error: Failed parsing SMARTS '[Q:1][C:2][C:3](=[O:4])[O:5]' for input: '[Q:1][C:2][C:3](=[O:4])[O:5]' 93: O=C1CNC(=O)CN1 -93: [00:24:56] product atom-mapping number 1 found multiple times. -93: [00:24:56] mapped atoms in the reactants were not mapped in the products. +93: [20:24:12] product atom-mapping number 1 found multiple times. +93: [20:24:12] mapped atoms in the reactants were not mapped in the products. 93: unmapped numbers are: 4 -93: [00:24:56] atom 0 in product 0 has multiple charge specifications. +93: [20:24:12] atom 0 in product 0 has multiple charge specifications. 93: mass: 15.0001 93: Oc1ccccn1 93: Oc1ccc[nH]1 -93: [00:24:56] SMARTS Parse Error: syntax error while parsing: ([C:1](=O)O.[C:2] -93: [00:24:56] SMARTS Parse Error: Failed parsing SMARTS '([C:1](=O)O.[C:2]' for input: '([C:1](=O)O.[C:2]' -93: [00:24:56] SMARTS Parse Error: syntax error while parsing: ([C:2] -93: [00:24:56] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' -93: [00:24:56] SMARTS Parse Error: syntax error while parsing: [C:1](=O)O).[C:2] -93: [00:24:56] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=O)O).[C:2]' for input: '[C:1](=O)O).[C:2]' -93: [00:24:56] SMARTS Parse Error: syntax error while parsing: [C:2]) -93: [00:24:56] SMARTS Parse Error: Failed parsing SMARTS '[C:2])' for input: '[C:2])' -93: [00:24:56] SMILES Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] -93: [00:24:56] SMILES Parse Error: check for mistakes around position 2: -93: [00:24:56] [Q:1][C:2][C:3](=[O:4])[O:5] -93: [00:24:56] ~^ -93: [00:24:56] SMILES Parse Error: Failed parsing SMILES '[Q:1][C:2][C:3](=[O:4])[O:5]' for input: '[Q:1][C:2][C:3](=[O:4])[O:5]' -93: [00:24:56] reactant 2 has no mapped atoms. -93: [00:24:56] >> Atoms within one molecule have different RXN roles. -93: [00:24:56] >> Fragment 0 not included in the reaction, atoms do not have a correct RXN role. -93: [00:24:56] SMARTS Parse Error: syntax error while parsing: ([C:1][C:2] -93: [00:24:56] SMARTS Parse Error: Failed parsing SMARTS '([C:1][C:2]' for input: '([C:1][C:2]' -93: [00:24:56] SMARTS Parse Error: syntax error while parsing: ([C:2] -93: [00:24:56] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' -93: [00:24:56] SMARTS Parse Error: syntax error while parsing: [C:1][C:2]) -93: [00:24:56] SMARTS Parse Error: Failed parsing SMARTS '[C:1][C:2])' for input: '[C:1][C:2])' -93: [00:24:56] SMARTS Parse Error: syntax error while parsing: [C:1]).[C:2] -93: [00:24:56] SMARTS Parse Error: Failed parsing SMARTS '[C:1]).[C:2]' for input: '[C:1]).[C:2]' -93: [00:24:56] reactant 0 has no mapped atoms. -93: [00:24:56] reactant 1 has no mapped atoms. -93: [00:24:56] reactant 3 has no mapped atoms. -93: [00:24:56] product atom-mapping number 2 found multiple times. -93: [00:24:56] product atom-mapping number 3 found multiple times. -93: [00:24:56] product atom-mapping number 4 found multiple times. -93: [00:24:56] product atom-mapping number 5 found multiple times. -93: [00:24:56] product atom-mapping number 6 found multiple times. -93: [00:24:56] product atom-mapping number 7 found multiple times. -93: [00:24:56] product atom-mapping number 8 found multiple times. -93: [00:24:56] product atom-mapping number 12 found multiple times. -93: [00:24:56] product atom-mapping number 9 found multiple times. -93: [00:24:56] product atom-mapping number 10 found multiple times. -93: [00:24:56] product atom-mapping number 11 found multiple times. -93: [00:24:56] reactant 0 has no mapped atoms. -93: [00:24:56] reactant 1 has no mapped atoms. -93: [00:24:56] reactant 3 has no mapped atoms. -93: [00:24:56] reactant atom-mapping number 19 found multiple times. -93: [00:24:56] reactant atom-mapping number 25 found multiple times. -93: [00:24:56] reactant atom-mapping number 20 found multiple times. -93: [00:24:56] reactant atom-mapping number 21 found multiple times. -93: [00:24:56] reactant atom-mapping number 22 found multiple times. -93: [00:24:56] reactant atom-mapping number 23 found multiple times. -93: [00:24:56] reactant atom-mapping number 24 found multiple times. -93: [00:24:56] product atom-mapping number 1 found multiple times. -93: [00:24:56] product atom-mapping number 1 found multiple times. -93: [00:24:56] product atom-mapping number 1 found multiple times. -93: [00:24:56] product atom-mapping number 1 found multiple times. -93: [00:24:56] product atom-mapping number 2 found multiple times. -93: [00:24:56] product atom-mapping number 1 found multiple times. -93: [00:24:56] product atom-mapping number 2 found multiple times. -93: [00:24:56] product atom-mapping number 1 found multiple times. -93: [00:24:56] product atom-mapping number 2 found multiple times. -93: [00:24:56] product atom-mapping number 1 found multiple times. -93: [00:24:56] product atom-mapping number 2 found multiple times. -93: [00:24:56] product atom-mapping number 1 found multiple times. +93: [20:24:12] SMARTS Parse Error: syntax error while parsing: ([C:1](=O)O.[C:2] +93: [20:24:12] SMARTS Parse Error: Failed parsing SMARTS '([C:1](=O)O.[C:2]' for input: '([C:1](=O)O.[C:2]' +93: [20:24:12] SMARTS Parse Error: syntax error while parsing: ([C:2] +93: [20:24:12] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' +93: [20:24:12] SMARTS Parse Error: syntax error while parsing: [C:1](=O)O).[C:2] +93: [20:24:12] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=O)O).[C:2]' for input: '[C:1](=O)O).[C:2]' +93: [20:24:12] SMARTS Parse Error: syntax error while parsing: [C:2]) +93: [20:24:12] SMARTS Parse Error: Failed parsing SMARTS '[C:2])' for input: '[C:2])' +93: [20:24:12] SMILES Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] +93: [20:24:12] SMILES Parse Error: check for mistakes around position 2: +93: [20:24:12] [Q:1][C:2][C:3](=[O:4])[O:5] +93: [20:24:12] ~^ +93: [20:24:12] SMILES Parse Error: Failed parsing SMILES '[Q:1][C:2][C:3](=[O:4])[O:5]' for input: '[Q:1][C:2][C:3](=[O:4])[O:5]' +93: [20:24:12] reactant 2 has no mapped atoms. +93: [20:24:12] >> Atoms within one molecule have different RXN roles. +93: [20:24:12] >> Fragment 0 not included in the reaction, atoms do not have a correct RXN role. +93: [20:24:12] SMARTS Parse Error: syntax error while parsing: ([C:1][C:2] +93: [20:24:12] SMARTS Parse Error: Failed parsing SMARTS '([C:1][C:2]' for input: '([C:1][C:2]' +93: [20:24:12] SMARTS Parse Error: syntax error while parsing: ([C:2] +93: [20:24:12] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' +93: [20:24:12] SMARTS Parse Error: syntax error while parsing: [C:1][C:2]) +93: [20:24:12] SMARTS Parse Error: Failed parsing SMARTS '[C:1][C:2])' for input: '[C:1][C:2])' +93: [20:24:12] SMARTS Parse Error: syntax error while parsing: [C:1]).[C:2] +93: [20:24:12] SMARTS Parse Error: Failed parsing SMARTS '[C:1]).[C:2]' for input: '[C:1]).[C:2]' +93: [20:24:12] reactant 0 has no mapped atoms. +93: [20:24:12] reactant 1 has no mapped atoms. +93: [20:24:12] reactant 3 has no mapped atoms. +93: [20:24:12] product atom-mapping number 2 found multiple times. +93: [20:24:12] product atom-mapping number 3 found multiple times. +93: [20:24:12] product atom-mapping number 4 found multiple times. +93: [20:24:12] product atom-mapping number 5 found multiple times. +93: [20:24:12] product atom-mapping number 6 found multiple times. +93: [20:24:12] product atom-mapping number 7 found multiple times. +93: [20:24:12] product atom-mapping number 8 found multiple times. +93: [20:24:12] product atom-mapping number 12 found multiple times. +93: [20:24:12] product atom-mapping number 9 found multiple times. +93: [20:24:12] product atom-mapping number 10 found multiple times. +93: [20:24:12] product atom-mapping number 11 found multiple times. +93: [20:24:12] reactant 0 has no mapped atoms. +93: [20:24:12] reactant 1 has no mapped atoms. +93: [20:24:12] reactant 3 has no mapped atoms. +93: [20:24:12] reactant atom-mapping number 19 found multiple times. +93: [20:24:12] reactant atom-mapping number 25 found multiple times. +93: [20:24:12] reactant atom-mapping number 20 found multiple times. +93: [20:24:12] reactant atom-mapping number 21 found multiple times. +93: [20:24:12] reactant atom-mapping number 22 found multiple times. +93: [20:24:12] reactant atom-mapping number 23 found multiple times. +93: [20:24:12] reactant atom-mapping number 24 found multiple times. +93: [20:24:12] product atom-mapping number 1 found multiple times. +93: [20:24:12] product atom-mapping number 1 found multiple times. +93: [20:24:12] product atom-mapping number 1 found multiple times. +93: [20:24:12] product atom-mapping number 1 found multiple times. +93: [20:24:12] product atom-mapping number 2 found multiple times. +93: [20:24:12] product atom-mapping number 1 found multiple times. +93: [20:24:12] product atom-mapping number 2 found multiple times. +93: [20:24:12] product atom-mapping number 1 found multiple times. +93: [20:24:12] product atom-mapping number 2 found multiple times. +93: [20:24:12] product atom-mapping number 1 found multiple times. +93: [20:24:12] product atom-mapping number 2 found multiple times. +93: [20:24:12] product atom-mapping number 1 found multiple times. 93: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br -93: [00:24:56] product atom-mapping number 2 found multiple times. -93: [00:24:56] product atom-mapping number 1 found multiple times. -93: [00:24:56] product atom-mapping number 2 found multiple times. -93: [00:24:56] product atom-mapping number 1 found multiple times. +93: [20:24:12] product atom-mapping number 2 found multiple times. +93: [20:24:12] product atom-mapping number 1 found multiple times. +93: [20:24:12] product atom-mapping number 2 found multiple times. +93: [20:24:12] product atom-mapping number 1 found multiple times. 93: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br -93: [00:24:56] product atom-mapping number 5 found multiple times. -93: [00:24:56] product atom-mapping number 2 found multiple times. -93: [00:24:56] product atom-mapping number 3 found multiple times. -93: [00:24:56] product atom-mapping number 1 found multiple times. -93: [00:24:56] product atom-mapping number 4 found multiple times. -93: [00:24:56] product atom-mapping number 5 found multiple times. -93: [00:24:56] product atom-mapping number 2 found multiple times. -93: [00:24:56] product atom-mapping number 3 found multiple times. -93: [00:24:56] product atom-mapping number 1 found multiple times. -93: [00:24:56] product atom-mapping number 4 found multiple times. +93: [20:24:12] product atom-mapping number 5 found multiple times. +93: [20:24:12] product atom-mapping number 2 found multiple times. +93: [20:24:12] product atom-mapping number 3 found multiple times. +93: [20:24:12] product atom-mapping number 1 found multiple times. +93: [20:24:12] product atom-mapping number 4 found multiple times. +93: [20:24:12] product atom-mapping number 5 found multiple times. +93: [20:24:12] product atom-mapping number 2 found multiple times. +93: [20:24:12] product atom-mapping number 3 found multiple times. +93: [20:24:12] product atom-mapping number 1 found multiple times. +93: [20:24:12] product atom-mapping number 4 found multiple times. 93: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br -93: [00:24:56] product atom-mapping number 5 found multiple times. -93: [00:24:56] product atom-mapping number 2 found multiple times. -93: [00:24:56] product atom-mapping number 3 found multiple times. -93: [00:24:56] product atom-mapping number 1 found multiple times. -93: [00:24:56] product atom-mapping number 4 found multiple times. -93: [00:24:56] product atom-mapping number 5 found multiple times. -93: [00:24:56] product atom-mapping number 2 found multiple times. -93: [00:24:56] product atom-mapping number 3 found multiple times. -93: [00:24:56] product atom-mapping number 1 found multiple times. -93: [00:24:56] product atom-mapping number 4 found multiple times. +93: [20:24:12] product atom-mapping number 5 found multiple times. +93: [20:24:12] product atom-mapping number 2 found multiple times. +93: [20:24:12] product atom-mapping number 3 found multiple times. +93: [20:24:12] product atom-mapping number 1 found multiple times. +93: [20:24:12] product atom-mapping number 4 found multiple times. +93: [20:24:12] product atom-mapping number 5 found multiple times. +93: [20:24:12] product atom-mapping number 2 found multiple times. +93: [20:24:12] product atom-mapping number 3 found multiple times. +93: [20:24:12] product atom-mapping number 1 found multiple times. +93: [20:24:12] product atom-mapping number 4 found multiple times. 93: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br -93: [00:24:56] product atom-mapping number 2 found multiple times. -93: [00:24:56] product atom-mapping number 3 found multiple times. -93: [00:24:56] product atom-mapping number 1 found multiple times. -93: [00:24:56] product atom-mapping number 4 found multiple times. -93: [00:24:56] product atom-mapping number 2 found multiple times. -93: [00:24:56] product atom-mapping number 3 found multiple times. -93: [00:24:56] product atom-mapping number 1 found multiple times. -93: [00:24:56] product atom-mapping number 4 found multiple times. +93: [20:24:12] product atom-mapping number 2 found multiple times. +93: [20:24:12] product atom-mapping number 3 found multiple times. +93: [20:24:12] product atom-mapping number 1 found multiple times. +93: [20:24:12] product atom-mapping number 4 found multiple times. +93: [20:24:12] product atom-mapping number 2 found multiple times. +93: [20:24:12] product atom-mapping number 3 found multiple times. +93: [20:24:12] product atom-mapping number 1 found multiple times. +93: [20:24:12] product atom-mapping number 4 found multiple times. 93: F[C@@](Cl)(Br)O[C@](F)(Cl)Br -93: [00:24:56] product atom-mapping number 2 found multiple times. -93: [00:24:56] product atom-mapping number 3 found multiple times. -93: [00:24:56] product atom-mapping number 1 found multiple times. -93: [00:24:56] product atom-mapping number 4 found multiple times. -93: [00:24:56] product atom-mapping number 2 found multiple times. -93: [00:24:56] product atom-mapping number 3 found multiple times. -93: [00:24:56] product atom-mapping number 1 found multiple times. -93: [00:24:56] product atom-mapping number 4 found multiple times. +93: [20:24:12] product atom-mapping number 2 found multiple times. +93: [20:24:12] product atom-mapping number 3 found multiple times. +93: [20:24:12] product atom-mapping number 1 found multiple times. +93: [20:24:12] product atom-mapping number 4 found multiple times. +93: [20:24:12] product atom-mapping number 2 found multiple times. +93: [20:24:12] product atom-mapping number 3 found multiple times. +93: [20:24:12] product atom-mapping number 1 found multiple times. +93: [20:24:12] product atom-mapping number 4 found multiple times. 93: F[C@](Cl)(Br)O[C@](F)(Cl)Br -93: [00:24:56] product atom-mapping number 4 found multiple times. -93: [00:24:56] product atom-mapping number 3 found multiple times. -93: [00:24:56] product atom-mapping number 2 found multiple times. -93: [00:24:56] product atom-mapping number 1 found multiple times. -93: [00:24:56] product atom-mapping number 4 found multiple times. -93: [00:24:56] product atom-mapping number 3 found multiple times. -93: [00:24:56] product atom-mapping number 2 found multiple times. -93: [00:24:56] product atom-mapping number 1 found multiple times. -93: [00:24:56] product atom-mapping number 4 found multiple times. -93: [00:24:56] product atom-mapping number 3 found multiple times. -93: [00:24:56] product atom-mapping number 2 found multiple times. -93: [00:24:56] product atom-mapping number 1 found multiple times. -93: [00:24:56] product atom-mapping number 4 found multiple times. -93: [00:24:56] product atom-mapping number 3 found multiple times. -93: [00:24:56] product atom-mapping number 2 found multiple times. -93: [00:24:56] product atom-mapping number 1 found multiple times. -93: [00:24:56] product atom-mapping number 3 found multiple times. -93: [00:24:56] product atom-mapping number 2 found multiple times. -93: [00:24:56] product atom-mapping number 1 found multiple times. -93: [00:24:56] mapped atoms in the reactants were not mapped in the products. +93: [20:24:12] product atom-mapping number 4 found multiple times. +93: [20:24:12] product atom-mapping number 3 found multiple times. +93: [20:24:12] product atom-mapping number 2 found multiple times. +93: [20:24:12] product atom-mapping number 1 found multiple times. +93: [20:24:12] product atom-mapping number 4 found multiple times. +93: [20:24:12] product atom-mapping number 3 found multiple times. +93: [20:24:12] product atom-mapping number 2 found multiple times. +93: [20:24:12] product atom-mapping number 1 found multiple times. +93: [20:24:12] product atom-mapping number 4 found multiple times. +93: [20:24:12] product atom-mapping number 3 found multiple times. +93: [20:24:12] product atom-mapping number 2 found multiple times. +93: [20:24:12] product atom-mapping number 1 found multiple times. +93: [20:24:12] product atom-mapping number 4 found multiple times. +93: [20:24:12] product atom-mapping number 3 found multiple times. +93: [20:24:12] product atom-mapping number 2 found multiple times. +93: [20:24:12] product atom-mapping number 1 found multiple times. +93: [20:24:12] product atom-mapping number 3 found multiple times. +93: [20:24:12] product atom-mapping number 2 found multiple times. +93: [20:24:12] product atom-mapping number 1 found multiple times. +93: [20:24:12] mapped atoms in the reactants were not mapped in the products. 93: unmapped numbers are: 4 -93: [00:24:56] product atom-mapping number 3 found multiple times. -93: [00:24:56] product atom-mapping number 2 found multiple times. -93: [00:24:56] product atom-mapping number 1 found multiple times. -93: [00:24:56] mapped atoms in the reactants were not mapped in the products. +93: [20:24:12] product atom-mapping number 3 found multiple times. +93: [20:24:12] product atom-mapping number 2 found multiple times. +93: [20:24:12] product atom-mapping number 1 found multiple times. +93: [20:24:12] mapped atoms in the reactants were not mapped in the products. 93: unmapped numbers are: 4 -93: [00:24:56] product atom-mapping number 6 not found in reactants. -93: [00:24:56] product atom-mapping number 7 not found in reactants. -93: [00:24:56] product atom-mapping number 8 not found in reactants. -93: [00:24:56] product atom-mapping number 7 not found in reactants. -93: [00:24:56] product atom-mapping number 8 not found in reactants. -93: [00:24:56] product atom-mapping number 9 not found in reactants. -93: [00:24:56] product atom-mapping number 10 not found in reactants. -93: [00:24:56] mapped atoms in the reactants were not mapped in the products. +93: [20:24:12] product atom-mapping number 6 not found in reactants. +93: [20:24:12] product atom-mapping number 7 not found in reactants. +93: [20:24:12] product atom-mapping number 8 not found in reactants. +93: [20:24:12] product atom-mapping number 7 not found in reactants. +93: [20:24:12] product atom-mapping number 8 not found in reactants. +93: [20:24:12] product atom-mapping number 9 not found in reactants. +93: [20:24:12] product atom-mapping number 10 not found in reactants. +93: [20:24:12] mapped atoms in the reactants were not mapped in the products. 93: unmapped numbers are: 6 -93: [00:24:56] product atom-mapping number 7 not found in reactants. -93: [00:24:56] product atom-mapping number 8 not found in reactants. -93: [00:24:56] product atom-mapping number 9 not found in reactants. -93: [00:24:56] product atom-mapping number 10 not found in reactants. -93: [00:24:56] mapped atoms in the reactants were not mapped in the products. +93: [20:24:12] product atom-mapping number 7 not found in reactants. +93: [20:24:12] product atom-mapping number 8 not found in reactants. +93: [20:24:12] product atom-mapping number 9 not found in reactants. +93: [20:24:12] product atom-mapping number 10 not found in reactants. +93: [20:24:12] 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] -93: [00:24:56] mapped atoms in the reactants were not mapped in the products. +94: [20:24:12] ------------------------------------- +94: [20:24:12] Test Reaction StructuralFingerprint +94: [20:24:12] ------------------------------------- +94: [20:24:12] Test Reaction DifferenceFingerprint +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 +72: [20:24:12] ERROR: Cannot convert 'foo' to unsigned int on line 557 +72: [20:24:12] ERROR: moving to the beginning of the next molecule +72: [20:24:12] Finished: testIssue3525673() +72: [20:24:12] ----------------------------------------- +72: +72: [20:24:12] ----------------------------------------- +72: [20:24:12] Finished: testBlankLinesInProps() +72: [20:24:12] ----------------------------------------- +72: +72: [20:24:12] ----------------------------------------- +72: [20:24:12] Finished: testSkipLines() +72: [20:24:12] ----------------------------------------- +72: +72: [20:24:12] ----------------------------------------- +72: [20:24:13] Finished: testGitHub23() +72: [20:24:13] ----------------------------------------- +72: +72: [20:24:13] ----------------------------------------- +72: [20:24:13] Finished: testGitHub88() +72: [20:24:13] ----------------------------------------- +72: +72: [20:24:13] ----------------------------------------- +72: [20:24:13] Finished: testGitHub2285() +72: [20:24:13] ----------------------------------------- +72: +72: [20:24:13] ----------------------------------------- +72: [20:24:13] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +72: [20:24:13] ERROR: Smiles parse error on line 1 +72: [20:24:13] ERROR: Cannot create molecule from : 'c1ccccc' +72: [20:24:13] SMILES Parse Error: extra open parentheses while parsing: C(C +72: [20:24:13] SMILES Parse Error: check for mistakes around position 2: +72: [20:24:13] C(C +72: [20:24:13] ~^ +72: [20:24:13] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' +72: [20:24:13] ERROR: Smiles parse error on line 3 +72: [20:24:13] ERROR: Cannot create molecule from : 'C(C' +72: [20:24:13] Explicit valence for atom # 1 C, 5, is greater than permitted +72: [20:24:13] ERROR: Could not sanitize molecule on line 5 +72: [20:24:13] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted +72: [20:24:13] Explicit valence for atom # 1 F, 2, is greater than permitted +72: [20:24:13] ERROR: Could not sanitize molecule ending on line 21 +72: [20:24:13] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +72: [20:24:13] Explicit valence for atom # 1 F, 2, is greater than permitted +72: [20:24:13] ERROR: Could not sanitize molecule ending on line 21 +72: [20:24:13] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +93: [20:24:13] 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 -83: Randomness seeded to: 612149153 -83: [00:24:56] Invalid or missing fragment id from CDXML fragment, assigning new one... -83: [00:24:56] Explicit valence for atom # 3 N, 4, is greater than permitted -83: [00:24:56] CDXMLParser: failed sanitizing skipping fragment 32 -83: [00:24:56] Bad bond in CDXML skipping fragment 58... -83: [00:24:56] Invalid or missing fragment id from CDXML fragment, assigning new one... -83: [00:24:56] Bad bond in CDXML skipping fragment 58... -83: [00:24:56] WARNING: not removing hydrogen atom without neighbors -83: [00:24:56] WARNING: not removing hydrogen atom without neighbors -83: [00:24:56] WARNING: not removing hydrogen atom without neighbors -83: [00:24:56] WARNING: not removing hydrogen atom without neighbors -83: [00:24:56] WARNING: not removing hydrogen atom without neighbors -83: [00:24:56] WARNING: not removing hydrogen atom without neighbors -83: [00:24:56] WARNING: not removing hydrogen atom without neighbors -83: [00:24:56] WARNING: not removing hydrogen atom without neighbors -83: [00:24:56] WARNING: not removing hydrogen atom without neighbors -83: [00:24:56] WARNING: not removing hydrogen atom without neighbors -83: [00:24:56] CDXMLParser: Schema 80180 step 80181 ReactionStepAgents reaction fragment 64603 not found in document. -83: [00:24:56] Incomplete atom labelling, cannot make bond -83: [00:24:56] Incomplete atom labelling, cannot make bond -83: [00:24:56] Incomplete atom labelling, cannot make bond -83: [00:24:56] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas -83: [00:24:56] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas -83: [00:24:56] Failed to parse XML fragment 5 node: b attribute: Order: slartibartfast -83: [00:24:56] Failed to parse XML fragment 5 node: b attribute: Order: 5 -83: [00:24:56] Invalid or missing fragment id from CDXML fragment, assigning new one... +83: [20:24:12] Incomplete atom labelling, cannot make bond +83: [20:24:12] Incomplete atom labelling, cannot make bond +83: [20:24:12] Incomplete atom labelling, cannot make bond +83: [20:24:12] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas +83: [20:24:12] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas +83: [20:24:12] Failed to parse XML fragment 5 node: b attribute: Order: slartibartfast +83: [20:24:12] Failed to parse XML fragment 5 node: b attribute: Order: 5 +83: [20:24:12] Invalid or missing fragment id from CDXML fragment, assigning new one... 83: =============================================================================== 83: All tests passed (263 assertions in 7 test cases) 83: -test 112 - Start 112: testAUTOCORR2D - -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 -60: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [00:24:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: Test -60: -60: Sotorasib_atropBad1.cxsmi -60: -60: [00:24:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -60: [00:24:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -60: [00:24:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -60: [00:24:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -60: [00:24:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -60: Test -60: -60: Sotorasib_atropBad2.cxsmi -60: -60: [00:24:56] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -60: [00:24:56] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -60: [00:24:56] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -60: [00:24:56] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -60: [00:24:56] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -72: [00:24:56] Finished: testGetItemText() -72: [00:24:56] ----------------------------------------- -72: -72: [00:24:56] ----------------------------------------- -93: [00:24:56] product atom-mapping number 17 not found in reactants. -93: [00:24:56] product atom-mapping number 18 not found in reactants. -93: [00:24:56] mapped atoms in the reactants were not mapped in the products. -93: unmapped numbers are: 12 -96: Randomness seeded to: 715535639 -96: [00:24:56] atom 0 in product 0 has multiple charge specifications. -96: [00:24:56] Found a SCD/SED line with missing/empty SDT specification at line 34 -96: [00:24:56] Found a SCD/SED line with missing/empty SDT specification at line 36 -96: [00:24:56] Found a SCD/SED line with missing/empty SDT specification at line 38 -96: [00:24:56] Found a SCD/SED line with missing/empty SDT specification at line 40 -96: [00:24:56] Found a SCD/SED line with missing/empty SDT specification at line 42 -96: [00:24:56] Found a SCD/SED line with missing/empty SDT specification at line 87 -96: [00:24:56] Found a SCD/SED line with missing/empty SDT specification at line 89 -96: [00:24:56] Found a SCD/SED line with missing/empty SDT specification at line 91 -96: [00:24:56] Found a SCD/SED line with missing/empty SDT specification at line 93 -96: [00:24:56] Found a SCD/SED line with missing/empty SDT specification at line 95 -96: [00:24:56] mapped atoms in the reactants were not mapped in the products. +96: Randomness seeded to: 3495070854 +96: [20:24:12] atom 0 in product 0 has multiple charge specifications. +96: [20:24:12] Found a SCD/SED line with missing/empty SDT specification at line 34 +96: [20:24:12] Found a SCD/SED line with missing/empty SDT specification at line 36 +96: [20:24:12] Found a SCD/SED line with missing/empty SDT specification at line 38 +96: [20:24:12] Found a SCD/SED line with missing/empty SDT specification at line 40 +96: [20:24:12] Found a SCD/SED line with missing/empty SDT specification at line 42 +96: [20:24:12] Found a SCD/SED line with missing/empty SDT specification at line 87 +96: [20:24:12] Found a SCD/SED line with missing/empty SDT specification at line 89 +96: [20:24:12] Found a SCD/SED line with missing/empty SDT specification at line 91 +96: [20:24:12] Found a SCD/SED line with missing/empty SDT specification at line 93 +96: [20:24:12] Found a SCD/SED line with missing/empty SDT specification at line 95 +96: [20:24:12] mapped atoms in the reactants were not mapped in the products. 96: unmapped numbers are: 2 -96: [00:24:56] mapped atoms in the reactants were not mapped in the products. +96: [20:24:12] mapped atoms in the reactants were not mapped in the products. 96: unmapped numbers are: 2 -96: [00:24:56] SMARTS Parse Error: unclosed ring for input: 'CC1' -96: [00:24:56] SMILES Parse Error: unclosed ring for input: 'CC1' -96: [00:24:56] mapped atoms in the reactants were not mapped in the products. +96: [20:24:12] SMARTS Parse Error: unclosed ring for input: 'CC1' +96: [20:24:12] SMILES Parse Error: unclosed ring for input: 'CC1' +96: [20:24:12] mapped atoms in the reactants were not mapped in the products. 96: unmapped numbers are: 2 -96: [00:24:56] product atom-mapping number 2 not found in reactants. -96: [00:24:56] mapped atoms in the reactants were not mapped in the products. +96: [20:24:12] product atom-mapping number 2 not found in reactants. +96: [20:24:12] mapped atoms in the reactants were not mapped in the products. 96: unmapped numbers are: 2 -96: [00:24:56] product atom-mapping number 2 not found in reactants. -96: [00:24:56] CX Extensions: Substance group hierarchy is not always preserved. -96: [00:24:56] CX Extensions: Substance group hierarchy is not always preserved. -96: [00:24:56] reactant 0 has no mapped atoms. -96: [00:24:56] product 0 has no mapped atoms. -96: [00:24:56] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -96: [00:24:56] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -96: [00:24:56] Explicit valence for atom # 1 O, 5, is greater than permitted +96: [20:24:12] product atom-mapping number 2 not found in reactants. +96: [20:24:12] CX Extensions: Substance group hierarchy is not always preserved. +96: [20:24:12] CX Extensions: Substance group hierarchy is not always preserved. +96: [20:24:13] reactant 0 has no mapped atoms. +96: [20:24:13] product 0 has no mapped atoms. +96: [20:24:13] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +96: [20:24:13] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +96: [20:24:13] Explicit valence for atom # 1 O, 5, is greater than permitted 96: =============================================================================== 96: All tests passed (722 assertions in 30 test cases) 96: -89: Randomness seeded to: 933496905 -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:24:56] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -95: 30000000 30000000 -30: ......[00:24:56] Molecule does not have explicit Hs. Consider calling AddHs() -90: done -90: hits2: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 -90: processing2 -90: launch2 :0 -90: launch2 :1 -90: launch2 :2 -90: launch2 :3 -90: done -90: preprocessing 3 -90: hits3: 1110100011001000010011100110100011011000010101000100110010101111011100101000001111110000010100100110 -90: processing3 -90: launch3 :0 -90: launch3 :1 -90: launch3 :2 -90: launch3 :3 -35: [00:24:56] Maximum BFS search size exceeded. -35: This is likely due to a highly symmetric fused ring system. 100: 1 smi: CC 100: 1 smi: CC 100: 2 smi: CCO[C@H](N)P @@ -21176,11 +20978,11 @@ 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 -100: [00:24:56] SMARTS Parse Error: syntax error while parsing: bar -100: [00:24:56] SMARTS Parse Error: Failed parsing SMARTS 'bar' for input: 'bar' -101: Randomness seeded to: 2704808005 -101: [00:24:56] Incomplete atom labelling, cannot make bond -101: [00:24:56] +100: [20:24:12] SMARTS Parse Error: syntax error while parsing: bar +100: [20:24:12] SMARTS Parse Error: Failed parsing SMARTS 'bar' for input: 'bar' +101: Randomness seeded to: 2681363039 +101: [20:24:13] Incomplete atom labelling, cannot make bond +101: [20:24:13] 101: 101: **** 101: Invariant Violation @@ -21193,21 +20995,21 @@ 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# 0x0000558DD1624596 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 5# 0x0000558DD1676168 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x0000558DD1676C88 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x0000558DD1677100 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x0000558DD1648903 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x0000558DD1648C6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x0000558DD161875E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x00007F42BF033CA8 in /lib/x86_64-linux-gnu/libc.so.6 +101: 4# 0x000055D52CF2F596 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 5# 0x000055D52CF81168 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x000055D52CF81C88 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x000055D52CF82100 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x000055D52CF53903 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x000055D52CF53C6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x000055D52CF2375E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x00007F8EE9C33CA8 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# 0x0000558DD16187A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 13# 0x000055D52CF237A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- 101: **** 101: -101: [00:24:56] Incomplete atom labelling, cannot make bond -101: [00:24:56] +101: [20:24:13] Incomplete atom labelling, cannot make bond +101: [20:24:13] 101: 101: **** 101: Invariant Violation @@ -21220,21 +21022,102 @@ 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# 0x0000558DD1624596 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 5# 0x0000558DD1676168 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x0000558DD1676C88 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x0000558DD1677100 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x0000558DD1648903 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x0000558DD1648C6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x0000558DD161875E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x00007F42BF033CA8 in /lib/x86_64-linux-gnu/libc.so.6 +101: 4# 0x000055D52CF2F596 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 5# 0x000055D52CF81168 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x000055D52CF81C88 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x000055D52CF82100 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x000055D52CF53903 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x000055D52CF53C6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x000055D52CF2375E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x00007F8EE9C33CA8 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# 0x0000558DD16187A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 13# 0x000055D52CF237A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- 101: **** 101: -101: [00:24:56] Incomplete atom labelling, cannot make bond -101: [00:24:56] +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 +106: Randomness seeded to: 3383607504 +106: --------- +106: =============================================================================== +106: All tests passed (11 assertions in 1 test case) +106: + 70/236 Test #83: cdxmlParserCatchTest ................... Passed 0.20 sec + 71/236 Test #94: testReactionFingerprints ............... Passed 0.13 sec + 72/236 Test #105: testSubgraphs2 ......................... Passed 0.06 sec + 73/236 Test #106: subgraphsCatch ......................... Passed 0.06 sec +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 + +111: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testDescriptors +111: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +111: Test timeout computed to be: 1500 +test 112 + Start 112: testAUTOCORR2D + +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 +72: [20:24:13] Explicit valence for atom # 1 F, 2, is greater than permitted +72: [20:24:13] ERROR: Could not sanitize molecule ending on line 21 +72: [20:24:13] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +72: [20:24:13] ERROR: Atom line too short: ' -9.6' on line 28 +72: [20:24:13] ERROR: moving to the beginning of the next molecule +72: [20:24:13] Explicit valence for atom # 1 F, 2, is greater than permitted +72: [20:24:13] ERROR: Could not sanitize molecule ending on line 21 +72: [20:24:13] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +72: [20:24:13] ERROR: Atom line too short: ' -9.6' on line 28 +72: [20:24:13] ERROR: moving to the beginning of the next molecule +72: [20:24:13] Finished: testGitHub2479() +72: [20:24:13] ----------------------------------------- +72: +72: [20:24:13] ----------------------------------------- +72: [20:24:13] Ignoring invalid chirality label: '7_S_8_9_6_10' +72: [20:24:13] Finished: testGitHub2881() +72: [20:24:13] ----------------------------------------- +72: +72: [20:24:13] ----------------------------------------- +72: [20:24:13] Finished: testGitHub3517() +72: [20:24:13] ----------------------------------------- +72: + 74/236 Test #72: testMolSupplier ........................ Passed 0.30 sec + 75/236 Test #96: rxnTestCatch ........................... Passed 0.16 sec + 76/236 Test #100: testChemTransforms ..................... Passed 0.13 sec +101: [20:24:13] Incomplete atom labelling, cannot make bond +101: [20:24:13] 101: 101: **** 101: Invariant Violation @@ -21247,23 +21130,23 @@ 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# 0x0000558DD1624596 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 5# 0x0000558DD1676168 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x0000558DD1676C88 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x0000558DD1677100 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x0000558DD1648903 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x0000558DD1648C6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x0000558DD161875E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x00007F42BF033CA8 in /lib/x86_64-linux-gnu/libc.so.6 +101: 4# 0x000055D52CF2F596 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 5# 0x000055D52CF81168 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x000055D52CF81C88 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x000055D52CF82100 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x000055D52CF53903 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x000055D52CF53C6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x000055D52CF2375E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x00007F8EE9C33CA8 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# 0x0000558DD16187A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 13# 0x000055D52CF237A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- 101: **** 101: -101: [00:24:56] Incomplete atom labelling, cannot make bond -101: [00:24:56] Incomplete atom labelling, cannot make bond -101: [00:24:56] Incomplete atom labelling, cannot make bond -101: [00:24:56] +101: [20:24:13] Incomplete atom labelling, cannot make bond +101: [20:24:13] Incomplete atom labelling, cannot make bond +101: [20:24:13] Incomplete atom labelling, cannot make bond +101: [20:24:13] 101: 101: **** 101: Invariant Violation @@ -21276,21 +21159,21 @@ 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# 0x0000558DD1624596 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 5# 0x0000558DD1676168 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x0000558DD1676C88 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x0000558DD1677100 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x0000558DD1648903 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x0000558DD1648C6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x0000558DD161875E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x00007F42BF033CA8 in /lib/x86_64-linux-gnu/libc.so.6 +101: 4# 0x000055D52CF2F596 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 5# 0x000055D52CF81168 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x000055D52CF81C88 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x000055D52CF82100 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x000055D52CF53903 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x000055D52CF53C6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x000055D52CF2375E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x00007F8EE9C33CA8 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# 0x0000558DD16187A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 13# 0x000055D52CF237A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- 101: **** 101: -101: [00:24:56] Incomplete atom labelling, cannot make bond -101: [00:24:56] +101: [20:24:13] Incomplete atom labelling, cannot make bond +101: [20:24:13] 101: 101: **** 101: Invariant Violation @@ -21303,20 +21186,20 @@ 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# 0x0000558DD1624596 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 5# 0x0000558DD1676168 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x0000558DD1676C88 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x0000558DD1677100 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x0000558DD1648903 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x0000558DD1648C6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x0000558DD161875E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x00007F42BF033CA8 in /lib/x86_64-linux-gnu/libc.so.6 +101: 4# 0x000055D52CF2F596 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 5# 0x000055D52CF81168 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x000055D52CF81C88 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x000055D52CF82100 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x000055D52CF53903 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x000055D52CF53C6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x000055D52CF2375E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x00007F8EE9C33CA8 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# 0x0000558DD16187A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 13# 0x000055D52CF237A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- 101: **** 101: -101: [00:24:56] +101: [20:24:13] 101: 101: **** 101: Invariant Violation @@ -21330,95 +21213,224 @@ 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# 0x0000558DD161987D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x0000558DD1676168 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x0000558DD1676C88 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x0000558DD1677100 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x0000558DD1648903 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x0000558DD1648C6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x0000558DD161875E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 12# 0x00007F42BF033CA8 in /lib/x86_64-linux-gnu/libc.so.6 +101: 5# 0x000055D52CF2487D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x000055D52CF81168 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x000055D52CF81C88 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x000055D52CF82100 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x000055D52CF53903 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x000055D52CF53C6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x000055D52CF2375E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 12# 0x00007F8EE9C33CA8 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# 0x0000558DD16187A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 14# 0x000055D52CF237A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- 101: **** 101: 101: =============================================================================== 101: All tests passed (675 assertions in 10 test cases) 101: -104: ----------------------- -104: Subgraph retrieval -104: Finished -104: ----------------------- -104: testSubgraphs2a -104: Finished -104: ----------------------- -104: testSubgraphs2 -104: Finished -104: ----------------------- -104: Path retrieval -104: Finished -104: ----------------------- -104: Path retrieval2 -104: Finished -104: ----------------------- -104: Unique Subgraph retrieval -104: Finished -104: ----------------------- -104: testUniqueSubgraphs2 -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 -106: Randomness seeded to: 1353519080 -106: --------- -106: =============================================================================== -106: All tests passed (11 assertions in 1 test case) -106: -109: 21 -111: [00:24:56] ------------------------------------- -111: [00:24:56] Test Crippen parameter acquisition. -111: [00:24:56] done -111: [00:24:56] ------------------------------------- -111: [00:24:56] Test Crippen calculation. -111: [00:24:56] done -111: [00:24:56] ------------------------------------- -111: [00:24:56] Test Issue262: problems with Crippen calculation from pickles. -111: [00:24:56] done -111: [00:24:56] ------------------------------------- -111: [00:24:56] Test AMW calculation. -111: [00:24:56] done -111: [00:24:56] ------------------------------------- -111: [00:24:56] Test Exact MW calculation. -111: [00:24:56] done -111: [00:24:56] ------------------------------------- -111: [00:24:56] Test Labute ASA descriptors. -111: [00:24:56] done -111: [00:24:56] ------------------------------------- -111: [00:24:56] Test TPSA descriptors. - 71/236 Test #83: cdxmlParserCatchTest ................... Passed 0.25 sec - 72/236 Test #96: rxnTestCatch ........................... Passed 0.19 sec - 73/236 Test #100: testChemTransforms ..................... Passed 0.17 sec - 74/236 Test #101: chemTransformsTestCatch ................ Passed 0.15 sec - 75/236 Test #105: testSubgraphs2 ......................... Passed 0.14 sec - 76/236 Test #106: subgraphsCatch ......................... Passed 0.14 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 +89: Randomness seeded to: 996548929 +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [20:24:13] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. test 114 Start 114: testBCUT @@ -21437,102 +21449,72 @@ 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 + 77/236 Test #101: chemTransformsTestCatch ................ Passed 0.13 sec +93: [20:24:13] product atom-mapping number 17 not found in reactants. +93: [20:24:13] product atom-mapping number 18 not found in reactants. +93: [20:24:13] mapped atoms in the reactants were not mapped in the products. +93: unmapped numbers are: 12 +95: 30000000 30000000 +104: Finished +104: ----------------------- +104: Path retrieval +104: Finished +104: ----------------------- +104: Path retrieval2 +104: Finished +104: ----------------------- +104: Unique Subgraph retrieval +104: Finished +104: ----------------------- +104: testUniqueSubgraphs2 +65: [20:24:13] Warning: stereochemistry around double bond may be incorrect in depiction. +109: 21 +70: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: Atropisomers- 1 hits 3 misses +70: Final results: +70: Found atropisomers in TestMultInSDF.sdf - 1 hits 4 misses +90: done +90: hits2: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 +90: processing2 +90: launch2 :0 +90: launch2 :1 +90: launch2 :2 +90: launch2 :3 +90: done +90: preprocessing 3 +90: hits3: 1110100011001000010011100110100011011000010101000100110010101111011100101000001111110000010100100110 +90: processing3 +90: launch3 :0 +90: launch3 :1 +90: launch3 :2 +90: launch3 :3 +111: [20:24:13] ------------------------------------- +111: [20:24:13] Test Crippen parameter acquisition. +111: [20:24:13] done +111: [20:24:13] ------------------------------------- +111: [20:24:13] Test Crippen calculation. +111: [20:24:13] done +111: [20:24:13] ------------------------------------- +111: [20:24:13] Test Issue262: problems with Crippen calculation from pickles. +111: [20:24:13] done +111: [20:24:13] ------------------------------------- +111: [20:24:13] Test AMW calculation. +111: [20:24:13] done +111: [20:24:13] ------------------------------------- +111: [20:24:13] Test Exact MW calculation. +111: [20:24:13] done +111: [20:24:13] ------------------------------------- +111: [20:24:13] Test Labute ASA descriptors. +111: [20:24:13] done +111: [20:24:13] ------------------------------------- +111: [20:24:13] Test TPSA descriptors. 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 - -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: [00:24:56] Finished: testForwardSDSupplier() -72: [00:24:56] ----------------------------------------- -72: -72: [00:24:56] ----------------------------------------- -72: [00:24:56] Finished: testMissingCRSDSupplier() -72: [00:24:56] ----------------------------------------- -72: -72: [00:24:56] ----------------------------------------- -72: [00:24:56] Finished: testIssue3482695() -72: [00:24:56] ----------------------------------------- -72: -72: [00:24:56] ----------------------------------------- -72: [00:24:56] ERROR: Cannot convert 'foo' to unsigned int on line 557 -72: [00:24:56] ERROR: moving to the beginning of the next molecule -72: [00:24:56] Finished: testIssue3525673() -72: [00:24:56] ----------------------------------------- -72: -72: [00:24:56] ----------------------------------------- -72: [00:24:56] Finished: testBlankLinesInProps() -72: [00:24:56] ----------------------------------------- -72: -72: [00:24:56] ----------------------------------------- -72: [00:24:56] Finished: testSkipLines() -72: [00:24:56] ----------------------------------------- -72: -72: [00:24:56] ----------------------------------------- -72: [00:24:56] Finished: testGitHub23() -72: [00:24:56] ----------------------------------------- -72: -72: [00:24:56] ----------------------------------------- -72: [00:24:56] Finished: testGitHub88() -72: [00:24:56] ----------------------------------------- -72: -72: [00:24:56] ----------------------------------------- -72: [00:24:56] Finished: testGitHub2285() -72: [00:24:56] ----------------------------------------- -72: -72: [00:24:56] ----------------------------------------- -72: [00:24:56] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -72: [00:24:56] ERROR: Smiles parse error on line 1 -72: [00:24:56] ERROR: Cannot create molecule from : 'c1ccccc' -72: [00:24:56] SMILES Parse Error: extra open parentheses while parsing: C(C -72: [00:24:56] SMILES Parse Error: check for mistakes around position 2: -72: [00:24:56] C(C -72: [00:24:56] ~^ -72: [00:24:56] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' -72: [00:24:56] ERROR: Smiles parse error on line 3 -72: [00:24:56] ERROR: Cannot create molecule from : 'C(C' -72: [00:24:56] Explicit valence for atom # 1 C, 5, is greater than permitted -72: [00:24:56] ERROR: Could not sanitize molecule on line 5 -72: [00:24:56] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted -72: [00:24:56] Explicit valence for atom # 1 F, 2, is greater than permitted -72: [00:24:56] ERROR: Could not sanitize molecule ending on line 21 -72: [00:24:56] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -72: [00:24:56] Explicit valence for atom # 1 F, 2, is greater than permitted -72: [00:24:56] ERROR: Could not sanitize molecule ending on line 21 -72: [00:24:56] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -72: [00:24:56] Explicit valence for atom # 1 F, 2, is greater than permitted -72: [00:24:56] ERROR: Could not sanitize molecule ending on line 21 -72: [00:24:56] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -72: [00:24:56] ERROR: Atom line too short: ' -9.6' on line 28 -72: [00:24:56] ERROR: moving to the beginning of the next molecule -72: [00:24:56] Explicit valence for atom # 1 F, 2, is greater than permitted -72: [00:24:56] ERROR: Could not sanitize molecule ending on line 21 -72: [00:24:56] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -72: [00:24:56] ERROR: Atom line too short: ' -9.6' on line 28 -72: [00:24:56] ERROR: moving to the beginning of the next molecule -72: [00:24:56] Finished: testGitHub2479() -72: [00:24:56] ----------------------------------------- -72: -72: [00:24:56] ----------------------------------------- -72: [00:24:56] Ignoring invalid chirality label: '7_S_8_9_6_10' -72: [00:24:56] Finished: testGitHub2881() -72: [00:24:56] ----------------------------------------- -72: -72: [00:24:56] ----------------------------------------- -72: [00:24:56] Finished: testGitHub3517() -72: [00:24:56] ----------------------------------------- -72: -80: [00:24:56] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -80: [00:24:56] 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.[00:24:56] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -80: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -80: [00:24:56] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -80: [00:24:56] 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) 107: v = { @@ -21621,106 +21603,585 @@ 107: 10,15}, 107: 11,16}, 107: } -112: [00:24:56] ---------------------------- +112: [20:24:13] ---------------------------- 112: start test autocorr2D -91: Randomness seeded to: 2920174783 -91: =============================================================================== -91: All tests passed (242 assertions in 12 test cases) -91: -70: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -111: [00:24:56] done -111: [00:24:56] ------------------------------------- -111: [00:24:56] Test Lipinski parameters. -114: [00:24:56] ------------------------------------- -114: [00:24:56] Basic BCUT tests. - 77/236 Test #72: testMolSupplier ........................ Passed 0.36 sec - 78/236 Test #91: substructTestCatch ..................... Passed 0.27 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 -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 +75: [20:24:13] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +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 +75: [20:24:13] bond with order 0 found on line 11. This is not part of the MDL specification. +75: [20:24:13] bond with order 0 found on line 16. This is not part of the MDL specification. 60: Test 60: -60: Sotorasib_3d.cxsmi +60: RP-6306_3d.cxsmi 60: 60: Test 60: -60: ZM374979_atrop1.cxsmi +60: Sotorasib_atrop1.cxsmi 60: 60: Test 60: -60: ZM374979_atrop2.cxsmi +60: Sotorasib_atrop2.cxsmi 60: 60: Test 60: -60: ZM374979_atrop3.cxsmi +60: Sotorasib_atrop3.cxsmi 60: 60: Test 60: -60: ZM374979_atrop4.cxsmi +60: Sotorasib_atrop4.cxsmi 60: 60: Test 60: -60: ZM374979_atropBad1.cxsmi +60: Sotorasib_atrop5.cxsmi 60: -60: [00:24:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -60: [00:24:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -60: [00:24:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -60: [00:24:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -60: [00:24:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 - 79/236 Test #113: testATF ................................ Passed 0.05 sec -116: [00:24:56] ------------------------------------- -116: [00:24:56] Basic PBF tests. -114: [00:24:56] done -114: [00:24:56] ------------------------------------- -114: [00:24:56] Larger BCUT tests. +60: [20:24:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [20:24:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [20:24:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [20:24:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [20:24:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [20:24:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [20:24:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [20:24:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [20:24:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [20:24:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: Test +60: +60: Sotorasib_atropBad1.cxsmi +60: +60: [20:24:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +60: [20:24:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +60: [20:24:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +60: [20:24:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 + 78/236 Test #70: testAtropisomers ....................... Passed 0.38 sec + 79/236 Test #113: testATF ................................ Passed 0.04 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 +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 +60: [20:24:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +60: Test +60: +60: Sotorasib_atropBad2.cxsmi +60: +60: [20:24:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +60: [20:24:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +60: [20:24:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +60: [20:24:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +60: [20:24:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +114: [20:24:13] ------------------------------------- +114: [20:24:13] Basic BCUT tests. +114: [20:24:13] done +114: [20:24:13] ------------------------------------- +114: [20:24:13] Larger BCUT tests. +116: [20:24:13] ------------------------------------- +116: [20:24:13] Basic PBF tests. +115: =>start test EEM +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: 0 +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +93: [20:24:13] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) +93: [20:24:13] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) +93: +93: [20:24:13] Mismatched potential rlabels: 1 unmapped reactant dummy atom rlabels,0 unmappped product dummy atom rlabels +93: ------------- +93: CCOc1ccccc1 +111: [20:24:13] done +111: [20:24:13] ------------------------------------- +111: [20:24:13] Test Lipinski parameters. + 80/236 Test #65: testDepictor ........................... Passed 0.44 sec + 81/236 Test #75: testMolWriter .......................... Passed 0.36 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 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 -70: Atropisomers- 1 hits 3 misses -70: Final results: -70: Found atropisomers in TestMultInSDF.sdf - 1 hits 4 misses +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +120: [20:24:13] ------------------------------------- +120: [20:24:13] Basic PMI tests. +30: ......[20:24:13] Molecule does not have explicit Hs. Consider calling AddHs() +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +91: Randomness seeded to: 800518692 +91: =============================================================================== +91: All tests passed (242 assertions in 12 test cases) +91: +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +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: [20:24:13] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +68: [20:24:13] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 90: done -90: [00:24:56] done -90: [00:24:56] ------------------------------------- -90: [00:24:56] Test GitHub issue 15 -90: [00:24:56] done -90: [00:24:56] ------------------------------------- -90: [00:24:56] Test GitHub issue 409 -90: [00:24:56] done -90: [00:24:56] ------------------------------------- -90: [00:24:56] Test chiral matching -90: [00:24:56] done -90: [00:24:56] ------------------------------------- -90: [00:24:56] Test GitHub issue 688: partially specified chiral substructure queries don't work properly -90: [00:24:56] done -90: [00:24:56] ------------------------------------- -90: [00:24:56] Test dative-bond matching -90: [00:24:56] done -90: [00:24:56] ------------------------------------- -90: [00:24:56] Test cis/trans matching -90: [00:24:56] done -90: [00:24:56] ------------------------------------- -90: [00:24:56] Test cis/trans matching part 2 -90: [00:24:56] done -90: [00:24:56] ------------------------------------- -90: [00:24:56] Testing Github #1389: Substructure matching with chirality failure when query is built from SMARTS -90: [00:24:56] done -90: [00:24:56] ------------------------------------- -90: [00:24:56] Testing matching E/Z against Cis/Trans stereo bonds -90: [00:24:56] +90: [20:24:13] done +90: [20:24:13] ------------------------------------- +90: [20:24:13] Test GitHub issue 15 +90: [20:24:13] done +90: [20:24:13] ------------------------------------- +90: [20:24:13] Test GitHub issue 409 +90: [20:24:13] done +90: [20:24:13] ------------------------------------- +90: [20:24:13] Test chiral matching +90: [20:24:13] done +90: [20:24:13] ------------------------------------- +90: [20:24:13] Test GitHub issue 688: partially specified chiral substructure queries don't work properly +90: [20:24:13] done +90: [20:24:13] ------------------------------------- +90: [20:24:13] Test dative-bond matching +90: [20:24:13] done +90: [20:24:13] ------------------------------------- +90: [20:24:13] Test cis/trans matching +90: [20:24:13] done +90: [20:24:13] ------------------------------------- +90: [20:24:13] Test cis/trans matching part 2 +90: [20:24:13] done +90: [20:24:13] ------------------------------------- +90: [20:24:13] Testing Github #1389: Substructure matching with chirality failure when query is built from SMARTS +90: [20:24:13] done +102: Randomness seeded to: 2209110757 +102: =============================================================================== +102: All tests passed (93 assertions in 13 test cases) +102: +35: [20:24:13] Maximum BFS search size exceeded. +35: This is likely due to a highly symmetric fused ring system. + 82/236 Test #91: substructTestCatch ..................... Passed 0.30 sec + 83/236 Test #102: tautomerQueryTestCatch ................. Passed 0.23 sec +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +90: [20:24:13] ------------------------------------- +90: [20:24:13] Testing matching E/Z against Cis/Trans stereo bonds +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 +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 +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +90: [20:24:13] 90: 90: **** 90: Pre-condition Violation @@ -21733,15 +22194,15 @@ 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# 0x000055B14B08238A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -90: 5# 0x000055B14B072BF1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -90: 6# 0x00007FC2EC033CA8 in /lib/x86_64-linux-gnu/libc.so.6 +90: 4# 0x00005594E7AB438A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: 5# 0x00005594E7AA4BF1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: 6# 0x00007F9273633CA8 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# 0x000055B14B072D31 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: 8# 0x00005594E7AA4D31 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch 90: ---------- 90: **** 90: -90: [00:24:56] +90: [20:24:13] 90: 90: **** 90: Pre-condition Violation @@ -21754,522 +22215,373 @@ 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# 0x000055B14B06D420 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -90: 5# 0x000055B14B072BF1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -90: 6# 0x00007FC2EC033CA8 in /lib/x86_64-linux-gnu/libc.so.6 +90: 4# 0x00005594E7A9F420 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: 5# 0x00005594E7AA4BF1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: 6# 0x00007F9273633CA8 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# 0x000055B14B072D31 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: 8# 0x00005594E7AA4D31 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch 90: ---------- 90: **** 90: -90: [00:24:56] ------------------------------------- -90: [00:24:56] Test substructure matching with a pathological case for symmetric SSSR -90: [00:24:56] ------------------------------------- -90: [00:24:56] Test isAtomTerminalRGroupOrQueryHydrogen -120: [00:24:56] ------------------------------------- -120: [00:24:56] Basic PMI tests. -115: =>start test EEM -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: 0 -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -102: Randomness seeded to: 3790707793 -102: =============================================================================== -102: All tests passed (93 assertions in 13 test cases) -102: -93: [00:24:56] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) -93: [00:24:56] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) -93: -93: [00:24:56] Mismatched potential rlabels: 1 unmapped reactant dummy atom rlabels,0 unmappped product dummy atom rlabels -93: ------------- -93: CCOc1ccccc1 - 80/236 Test #70: testAtropisomers ....................... Passed 0.43 sec - 81/236 Test #90: testSubstructMatch ..................... Passed 0.38 sec - 82/236 Test #102: tautomerQueryTestCatch ................. Passed 0.29 sec -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] 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 -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 -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 -89: [00:24:56] Explicit valence for atom # 9 N, 5, is greater than permitted -104: Finished -104: ----------------------- -104: testRootedSubgraphs -104: Finished -104: ----------------------- -104: testRootedPaths -104: Finished - 83/236 Test #104: testSubgraphs1 ......................... Passed 0.31 sec +90: [20:24:13] ------------------------------------- +90: [20:24:13] Test substructure matching with a pathological case for symmetric SSSR +90: [20:24:13] ------------------------------------- +90: [20:24:13] Test isAtomTerminalRGroupOrQueryHydrogen + 84/236 Test #90: testSubstructMatch ..................... Passed 0.32 sec +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 60: Test 60: -60: Mrtx1719_3d.cxsmi +60: Sotorasib_3d.cxsmi 60: 60: Test 60: -60: Mrtx1719_atrop1.cxsmi +60: ZM374979_atrop1.cxsmi 60: 60: Test 60: -60: Mrtx1719_atrop2.cxsmi +60: ZM374979_atrop2.cxsmi 60: 60: Test 60: -60: Mrtx1719_atrop3.cxsmi +60: ZM374979_atrop3.cxsmi 60: 60: Test 60: -60: Mrtx1719_atrop4.cxsmi +60: ZM374979_atrop4.cxsmi 60: 60: Test 60: -60: Mrtx1719_atropBad1.cxsmi +60: ZM374979_atropBad1.cxsmi 60: -60: [00:24:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -60: [00:24:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -60: [00:24:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -60: [00:24:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -60: [00:24:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -111: [00:24:57] done -111: [00:24:57] ------------------------------------- -111: [00:24:57] Test VSA descriptors. -111: [00:24:57] done -111: [00:24:57] ------------------------------------- -111: [00:24:57] Test molecular formula calculation. -111: [00:24:57] done -111: [00:24:57] ------------------------------------- -111: [00:24:57] Test Issue 3415534. -111: [00:24:57] done -111: [00:24:57] ------------------------------------- -111: [00:24:57] Test Issue3433771: Bad definition for Crippen atom type O11. -111: [00:24:57] done -111: [00:24:57] ------------------------------------- -111: [00:24:57] Test multithreading -111: reading molecules -111: processing -111: launch :0 -111: launch :1 -111: launch :2 -111: launch :3 -103: ..... -103: ---------------------------------------------------------------------- -103: Ran 5 tests in 0.030s -103: -103: OK -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +60: [20:24:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +60: [20:24:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +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: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +60: [20:24:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +60: [20:24:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +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: [20:24:13] +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# 0x00005573B3C4F99F in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +68: 3# 0x00005573B3C5A69C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +68: 4# 0x00005573B3C47A5D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +68: 5# 0x00007FB7ACE33CA8 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# 0x00005573B3C47BE1 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 +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 +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +68: Test +68: +68: MarvinBadStereoGroupsAbs.mrv +68: +68: Unrecognized group definition +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +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 +115: [20:24:13] 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: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +60: [20:24:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: 100 -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] 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: Expected a connect string of "hh, ht, eu" for a SruSgroup definition in MRV file +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +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 +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +68: Test +68: +68: MarvinBadSupAttachOrder.mrv +68: +68: Order for an AttachmentPoint definition must be an integer in MRV file +124: ===================== Testing CoulombMat ======================= +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: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +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: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] 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 +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. + 85/236 Test #104: testSubgraphs1 ......................... Passed 0.28 sec +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 +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +108: :488: RuntimeWarning: to-Python converter for boost::shared_ptr already registered; second conversion method ignored. 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 -89: [00:24:57] Explicit valence for atom # 3 Al, 6, is greater than permitted - 84/236 Test #103: pyTautomerQuery ........................ Passed 0.36 sec - 85/236 Test #107: filterCatalogTest ...................... Passed 0.35 sec -108: :488: RuntimeWarning: to-Python converter for boost::shared_ptr already registered; second conversion method ignored. -98: [00:24:57] == testCartesianProduct -98: .[00:24:57] == testEnumerateLibrary -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 -97: ...[00:24:57] -97: -97: **** -97: Pre-condition Violation -97: getNumImplicitHs() called without preceding call to calcImplicitValence() -97: Violation occurred on line 301 in file ./Code/GraphMol/Atom.cpp -97: Failed Expression: d_implicitValence > -1 -97: ---------- -97: Stacktrace: -97: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -97: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -97: 2# RDKit::Atom::getNumImplicitHs() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -97: 3# RDKit::Atom::getTotalNumHs(bool) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -97: 4# Queries::EqualityQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 -97: 5# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -97: 6# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -97: 7# Queries::OrQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -97: 8# 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 -97: 9# 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 -97: 10# 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 -97: 11# 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 -97: 12# RDKit::detail::RecursiveMatcher(RDKit::ROMol const&, RDKit::ROMol const&, std::vector >&, std::map*, std::less, std::allocator*> > >&, RDKit::SubstructMatchParameters const&, std::vector >&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 13# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 14# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 15# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 16# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 17# 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 -97: 18# RDKit::ReactionRunnerUtils::getReactantMatchesToTemplate(RDKit::ROMol const&, RDKit::ROMol const&, unsigned int, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemReactions.so.1 -97: 19# RDKit::ReactionRunnerUtils::getReactantMatches(std::vector, std::allocator > > const&, RDKit::ChemicalReaction const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >, std::allocator, std::allocator > >, std::allocator, std::allocator > > > > > >&, unsigned int, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemReactions.so.1 -97: 20# RDKit::run_Reactants(RDKit::ChemicalReaction const&, std::vector, std::allocator > > const&, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemReactions.so.1 -97: 21# RDKit::ChemicalReaction::runReactants(std::vector, std::allocator > >, unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemReactions.so.1 -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# 0x00007F4C7D7A562C 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 -97: 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/Chem/rdChemReactions.so -97: 30# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::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 -97: 31# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::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 -97: 32# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::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: 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# 0x00007F4C7B3B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -97: 37# 0x00007F4C7B3B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -97: 38# 0x00007F4C7B3B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -97: 39# 0x00007F4C7B3B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -97: 40# 0x00007F4C7B3B7933 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# 0x00007F4C7D7A23C6 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 -97: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 51# 0x0000000000690C6F in /usr/bin/python3 -97: 52# 0x000000000062D590 in /usr/bin/python3 -97: 53# _PyObject_MakeTpCall in /usr/bin/python3 -97: 54# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 55# 0x00000000005CD3C9 in /usr/bin/python3 -97: 56# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 57# 0x0000000000690C6F in /usr/bin/python3 -97: 58# 0x000000000062D590 in /usr/bin/python3 -97: 59# _PyObject_MakeTpCall in /usr/bin/python3 -97: 60# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 61# 0x00000000005CD3C9 in /usr/bin/python3 -97: 62# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 63# 0x0000000000690C6F in /usr/bin/python3 -97: 64# 0x000000000062D590 in /usr/bin/python3 -97: 65# _PyObject_MakeTpCall in /usr/bin/python3 -97: 66# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 67# 0x00000000005A0A3C in /usr/bin/python3 -97: 68# _PyObject_MakeTpCall in /usr/bin/python3 -97: 69# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 70# PyEval_EvalCode in /usr/bin/python3 -97: 71# 0x00000000006AB8D1 in /usr/bin/python3 -97: 72# 0x00000000006A899C in /usr/bin/python3 -97: 73# 0x00000000006B9943 in /usr/bin/python3 -97: 74# 0x00000000006B93E3 in /usr/bin/python3 -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# 0x00007F4C7E1AACA8 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: [00:24:57] -97: -97: **** -97: Pre-condition Violation -97: getNumImplicitHs() called without preceding call to calcImplicitValence() -97: Violation occurred on line 301 in file ./Code/GraphMol/Atom.cpp -97: Failed Expression: d_implicitValence > -1 -97: ---------- -97: Stacktrace: -97: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -97: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -97: 2# RDKit::Atom::getNumImplicitHs() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -97: 3# RDKit::Atom::getTotalNumHs(bool) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -97: 4# Queries::EqualityQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 -97: 5# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -97: 6# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -97: 7# Queries::OrQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -97: 8# 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 -97: 9# 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 -97: 10# 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 -97: 11# 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 -97: 12# RDKit::detail::RecursiveMatcher(RDKit::ROMol const&, RDKit::ROMol const&, std::vector >&, std::map*, std::less, std::allocator*> > >&, RDKit::SubstructMatchParameters const&, std::vector >&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 13# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 14# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 15# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 16# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 17# 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 -97: 18# RDKit::ReactionRunnerUtils::getReactantMatchesToTemplate(RDKit::ROMol const&, RDKit::ROMol const&, unsigned int, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemReactions.so.1 -97: 19# RDKit::ReactionRunnerUtils::getReactantMatches(std::vector, std::allocator > > const&, RDKit::ChemicalReaction const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >, std::allocator, std::allocator > >, std::allocator, std::allocator > > > > > >&, unsigned int, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemReactions.so.1 -97: 20# RDKit::run_Reactants(RDKit::ChemicalReaction const&, std::vector, std::allocator > > const&, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemReactions.so.1 -97: 21# RDKit::ChemicalReaction::runReactants(std::vector, std::allocator > >, unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemReactions.so.1 -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# 0x00007F4C7D7A562C 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 -97: 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/Chem/rdChemReactions.so -97: 30# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::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 -97: 31# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::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 -97: 32# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::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: 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# 0x00007F4C7B3B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -97: 37# 0x00007F4C7B3B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -97: 38# 0x00007F4C7B3B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -97: 39# 0x00007F4C7B3B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -97: 40# 0x00007F4C7B3B7933 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# 0x00007F4C7D7A23C6 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 -97: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 51# 0x0000000000690C6F in /usr/bin/python3 -97: 52# 0x000000000062D590 in /usr/bin/python3 -97: 53# _PyObject_MakeTpCall in /usr/bin/python3 -97: 54# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 55# 0x00000000005CD3C9 in /usr/bin/python3 -97: 56# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 57# 0x0000000000690C6F in /usr/bin/python3 -97: 58# 0x000000000062D590 in /usr/bin/python3 -97: 59# _PyObject_MakeTpCall in /usr/bin/python3 -97: 60# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 61# 0x00000000005CD3C9 in /usr/bin/python3 -97: 62# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 63# 0x0000000000690C6F in /usr/bin/python3 -97: 64# 0x000000000062D590 in /usr/bin/python3 -97: 65# _PyObject_MakeTpCall in /usr/bin/python3 -97: 66# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 67# 0x00000000005A0A3C in /usr/bin/python3 -97: 68# _PyObject_MakeTpCall in /usr/bin/python3 -97: 69# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 70# PyEval_EvalCode in /usr/bin/python3 -97: 71# 0x00000000006AB8D1 in /usr/bin/python3 -97: 72# 0x00000000006A899C in /usr/bin/python3 -97: 73# 0x00000000006B9943 in /usr/bin/python3 -97: 74# 0x00000000006B93E3 in /usr/bin/python3 -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# 0x00007F4C7E1AACA8 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: .........[00:24:57] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -97: [00:24:57] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -97: [00:24:57] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -97: [00:24:57] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -97: .[00:24:57] product atom-mapping number 1 found multiple times. -97: [00:24:57] product atom-mapping number 1 found multiple times. -30: ... -30: ---------------------------------------------------------------------- -30: Ran 12 tests in 0.508s -30: -30: OK -65: [00:24:57] Warning: stereochemistry around double bond may be incorrect in depiction. -99: .[00:24:57] reactant 0 has no mapped atoms. -99: [00:24:57] product 0 has no mapped atoms. -99: [00:24:57] reactant 0 has no mapped atoms. -99: [00:24:57] product 0 has no mapped atoms. -99: .[00:24:57] reactant 0 has no mapped atoms. -99: [00:24:57] reactant 1 has no mapped atoms. -99: [00:24:57] product 0 has no mapped atoms. -99: [00:24:57] reactant 0 has no mapped atoms. -99: [00:24:57] reactant 1 has no mapped atoms. -99: [00:24:57] product 0 has no mapped atoms. -99: [00:24:57] reactant 0 has no mapped atoms. -99: [00:24:57] reactant 1 has no mapped atoms. -99: [00:24:57] product 0 has no mapped atoms. -99: [00:24:57] reactant 0 has no mapped atoms. -99: [00:24:57] reactant 1 has no mapped atoms. -99: [00:24:57] product 0 has no mapped atoms. -99: [00:24:57] reactant 0 has no mapped atoms. -99: [00:24:57] reactant 1 has no mapped atoms. -99: [00:24:57] product 0 has no mapped atoms. -99: [00:24:57] reactant 0 has no mapped atoms. -99: [00:24:57] reactant 1 has no mapped atoms. -99: [00:24:57] product 0 has no mapped atoms. -99: [00:24:57] reactant 0 has no mapped atoms. -99: [00:24:57] reactant 1 has no mapped atoms. -99: [00:24:57] product 0 has no mapped atoms. -99: [00:24:57] reactant 0 has no mapped atoms. -99: [00:24:57] reactant 1 has no mapped atoms. -99: [00:24:57] product 0 has no mapped atoms. -99: [00:24:57] reactant 0 has no mapped atoms. -99: [00:24:57] reactant 1 has no mapped atoms. -99: [00:24:57] product 0 has no mapped atoms. -99: [00:24:57] reactant 0 has no mapped atoms. -99: [00:24:57] reactant 1 has no mapped atoms. -99: [00:24:57] product 0 has no mapped atoms. -99: [00:24:57] reactant 0 has no mapped atoms. -99: [00:24:57] reactant 1 has no mapped atoms. -99: [00:24:57] product 0 has no mapped atoms. -99: [00:24:57] reactant 0 has no mapped atoms. -99: [00:24:57] reactant 1 has no mapped atoms. -99: [00:24:57] product 0 has no mapped atoms. -99: [00:24:57] reactant 0 has no mapped atoms. -99: [00:24:57] reactant 1 has no mapped atoms. -99: [00:24:57] product 0 has no mapped atoms. -99: [00:24:57] reactant 0 has no mapped atoms. -99: [00:24:57] reactant 1 has no mapped atoms. -99: [00:24:57] product 0 has no mapped atoms. + 86/236 Test #107: filterCatalogTest ...................... Passed 0.27 sec +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] 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 0.042s +103: +103: OK +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 +99: .[20:24:13] reactant 0 has no mapped atoms. +99: [20:24:13] product 0 has no mapped atoms. +99: [20:24:13] reactant 0 has no mapped atoms. +99: [20:24:13] product 0 has no mapped atoms. +99: .[20:24:13] reactant 0 has no mapped atoms. +99: [20:24:13] reactant 1 has no mapped atoms. +99: [20:24:13] product 0 has no mapped atoms. +99: [20:24:13] reactant 0 has no mapped atoms. +99: [20:24:13] reactant 1 has no mapped atoms. +99: [20:24:13] product 0 has no mapped atoms. +99: [20:24:13] reactant 0 has no mapped atoms. +99: [20:24:13] reactant 1 has no mapped atoms. +99: [20:24:13] product 0 has no mapped atoms. +99: [20:24:13] reactant 0 has no mapped atoms. +99: [20:24:13] reactant 1 has no mapped atoms. +99: [20:24:13] product 0 has no mapped atoms. +124: CM test 1 mat Done +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +99: [20:24:13] reactant 0 has no mapped atoms. +99: [20:24:13] reactant 1 has no mapped atoms. +99: [20:24:13] product 0 has no mapped atoms. +99: [20:24:13] reactant 0 has no mapped atoms. +99: [20:24:13] reactant 1 has no mapped atoms. +99: [20:24:13] product 0 has no mapped atoms. +99: [20:24:13] reactant 0 has no mapped atoms. +99: [20:24:13] reactant 1 has no mapped atoms. +99: [20:24:13] product 0 has no mapped atoms. +99: [20:24:13] reactant 0 has no mapped atoms. +99: [20:24:13] reactant 1 has no mapped atoms. +99: [20:24:13] product 0 has no mapped atoms. +99: [20:24:13] reactant 0 has no mapped atoms. +99: [20:24:13] reactant 1 has no mapped atoms. +99: [20:24:13] product 0 has no mapped atoms. + 87/236 Test #124: testCoulombMat ......................... Passed 0.06 sec +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +99: [20:24:13] reactant 0 has no mapped atoms. +99: [20:24:13] reactant 1 has no mapped atoms. +99: [20:24:13] product 0 has no mapped atoms. +99: [20:24:13] reactant 0 has no mapped atoms. +99: [20:24:13] reactant 1 has no mapped atoms. +99: [20:24:13] product 0 has no mapped atoms. +99: [20:24:13] reactant 0 has no mapped atoms. +99: [20:24:13] reactant 1 has no mapped atoms. +99: [20:24:13] product 0 has no mapped atoms. +99: [20:24:13] reactant 0 has no mapped atoms. +99: [20:24:13] reactant 1 has no mapped atoms. +99: [20:24:13] product 0 has no mapped atoms. +99: [20:24:13] reactant 0 has no mapped atoms. +99: [20:24:13] reactant 1 has no mapped atoms. +99: [20:24:13] product 0 has no mapped atoms. 99: () 99: ******************************************** 99: $RXN @@ -22633,16 +22945,16 @@ 99: 1 2 1 0 99: M ISO 2 1 1 2 2 99: M END -99: [00:24:57] reactant 0 has no mapped atoms. -99: [00:24:57] reactant 1 has no mapped atoms. -99: [00:24:57] product 0 has no mapped atoms. -99: [00:24:57] Could not find RLabel mapping for atom: 0 in template: 1 -99: [00:24:57] reactant 1 has no mapped atoms. -99: [00:24:57] reactant 1 has no mapped atoms. -99: [00:24:57] reactant 1 has no mapped atoms. +99: [20:24:13] reactant 0 has no mapped atoms. +99: [20:24:13] reactant 1 has no mapped atoms. +99: [20:24:13] product 0 has no mapped atoms. +99: [20:24:13] Could not find RLabel mapping for atom: 0 in template: 1 +99: [20:24:13] reactant 1 has no mapped atoms. +99: [20:24:13] reactant 1 has no mapped atoms. +99: [20:24:13] reactant 1 has no mapped atoms. 99: .. 99: ---------------------------------------------------------------------- -99: Ran 4 tests in 0.023s +99: Ran 4 tests in 0.024s 99: 99: OK 99: @@ -22699,143 +23011,374 @@ 99: M END 99: 99: $RXN Failed -124: ===================== Testing CoulombMat ======================= -124: CM test 1 mat Done - 86/236 Test #124: testCoulombMat ......................... Passed 0.06 sec -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -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 +98: [20:24:13] == testCartesianProduct +98: .[20:24:13] == testEnumerateLibrary +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 +67: ..............[20:24:13] SMILES Parse Error: syntax error while parsing: invalidsmiles +67: [20:24:13] SMILES Parse Error: check for mistakes around position 1: +67: [20:24:13] invalidsmiles +67: [20:24:13] ^ +67: [20:24:13] SMILES Parse Error: Failed parsing SMILES 'invalidsmiles' for input: 'invalidsmiles' 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: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +111: [20:24:13] done +111: [20:24:13] ------------------------------------- +111: [20:24:13] Test VSA descriptors. +111: [20:24:13] done +111: [20:24:13] ------------------------------------- +111: [20:24:13] Test molecular formula calculation. +111: [20:24:13] done +111: [20:24:13] ------------------------------------- +111: [20:24:13] Test Issue 3415534. +111: [20:24:13] done +111: [20:24:13] ------------------------------------- +111: [20:24:13] Test Issue3433771: Bad definition for Crippen atom type O11. +111: [20:24:13] done +111: [20:24:13] ------------------------------------- +111: [20:24:13] Test multithreading +111: reading molecules + 88/236 Test #103: pyTautomerQuery ........................ Passed 0.34 sec +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +97: ...[20:24:13] +97: +97: **** 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 -97: ................[00:24:57] mapped atoms in the reactants were not mapped in the products. -97: unmapped numbers are: 3 -97: [00:24:57] 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: [00:24:57] mapped atoms in the reactants were not mapped in the products. -97: unmapped numbers are: 3 -97: ..[00:24:57] reactant 2 has no mapped atoms. -97: [00:24:57] reactant 2 has no mapped atoms. -97: [00:24:57] product 1 has no mapped atoms. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 87/236 Test #99: pyChemReactionSanitize ................. Passed 0.42 sec -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] 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 +97: Failed Expression: d_implicitValence > -1 +97: ---------- +97: Stacktrace: +97: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +97: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +97: 2# RDKit::Atom::getNumImplicitHs() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +97: 3# RDKit::Atom::getTotalNumHs(bool) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +97: 4# Queries::EqualityQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 +97: 5# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +97: 6# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +97: 7# Queries::OrQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +97: 8# 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 +97: 9# 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 +97: 10# 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 +97: 11# 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 +97: 12# RDKit::detail::RecursiveMatcher(RDKit::ROMol const&, RDKit::ROMol const&, std::vector >&, std::map*, std::less, std::allocator*> > >&, RDKit::SubstructMatchParameters const&, std::vector >&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 13# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 14# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 15# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 16# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 17# 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 +97: 18# RDKit::ReactionRunnerUtils::getReactantMatchesToTemplate(RDKit::ROMol const&, RDKit::ROMol const&, unsigned int, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemReactions.so.1 +97: 19# RDKit::ReactionRunnerUtils::getReactantMatches(std::vector, std::allocator > > const&, RDKit::ChemicalReaction const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >, std::allocator, std::allocator > >, std::allocator, std::allocator > > > > > >&, unsigned int, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemReactions.so.1 +97: 20# RDKit::run_Reactants(RDKit::ChemicalReaction const&, std::vector, std::allocator > > const&, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemReactions.so.1 +97: 21# RDKit::ChemicalReaction::runReactants(std::vector, std::allocator > >, unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemReactions.so.1 +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# 0x00007FEBAF21B62C 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 +97: 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/Chem/rdChemReactions.so +97: 30# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::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 +97: 31# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::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 +97: 32# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::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: 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# 0x00007FEBACDB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +97: 37# 0x00007FEBACDB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +97: 38# 0x00007FEBACDB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +97: 39# 0x00007FEBACDB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +97: 40# 0x00007FEBACDB7933 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# 0x00007FEBAF2183C6 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 +97: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 51# 0x0000000000690C6F in /usr/bin/python3 +97: 52# 0x000000000062D590 in /usr/bin/python3 +97: 53# _PyObject_MakeTpCall in /usr/bin/python3 +97: 54# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 55# 0x00000000005CD3C9 in /usr/bin/python3 +97: 56# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 57# 0x0000000000690C6F in /usr/bin/python3 +97: 58# 0x000000000062D590 in /usr/bin/python3 +97: 59# _PyObject_MakeTpCall in /usr/bin/python3 +97: 60# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 61# 0x00000000005CD3C9 in /usr/bin/python3 +97: 62# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 63# 0x0000000000690C6F in /usr/bin/python3 +97: 64# 0x000000000062D590 in /usr/bin/python3 +97: 65# _PyObject_MakeTpCall in /usr/bin/python3 +97: 66# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 67# 0x00000000005A0A3C in /usr/bin/python3 +97: 68# _PyObject_MakeTpCall in /usr/bin/python3 +97: 69# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 70# PyEval_EvalCode in /usr/bin/python3 +97: 71# 0x00000000006AB8D1 in /usr/bin/python3 +97: 72# 0x00000000006A899C in /usr/bin/python3 +97: 73# 0x00000000006B9943 in /usr/bin/python3 +97: 74# 0x00000000006B93E3 in /usr/bin/python3 +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# 0x00007FEBAFC20CA8 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: [20:24:13] +97: +97: **** +97: Pre-condition Violation +97: getNumImplicitHs() called without preceding call to calcImplicitValence() +97: Violation occurred on line 301 in file ./Code/GraphMol/Atom.cpp +97: Failed Expression: d_implicitValence > -1 +97: ---------- +97: Stacktrace: +97: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +97: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +97: 2# RDKit::Atom::getNumImplicitHs() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +97: 3# RDKit::Atom::getTotalNumHs(bool) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +97: 4# Queries::EqualityQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 +97: 5# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +97: 6# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +97: 7# Queries::OrQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +97: 8# 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 +97: 9# 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 +97: 10# 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 +97: 11# 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 +97: 12# RDKit::detail::RecursiveMatcher(RDKit::ROMol const&, RDKit::ROMol const&, std::vector >&, std::map*, std::less, std::allocator*> > >&, RDKit::SubstructMatchParameters const&, std::vector >&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 13# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 14# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 15# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 16# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 17# 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 +97: 18# RDKit::ReactionRunnerUtils::getReactantMatchesToTemplate(RDKit::ROMol const&, RDKit::ROMol const&, unsigned int, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemReactions.so.1 +97: 19# RDKit::ReactionRunnerUtils::getReactantMatches(std::vector, std::allocator > > const&, RDKit::ChemicalReaction const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >, std::allocator, std::allocator > >, std::allocator, std::allocator > > > > > >&, unsigned int, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemReactions.so.1 +97: 20# RDKit::run_Reactants(RDKit::ChemicalReaction const&, std::vector, std::allocator > > const&, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemReactions.so.1 +97: 21# RDKit::ChemicalReaction::runReactants(std::vector, std::allocator > >, unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemReactions.so.1 +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# 0x00007FEBAF21B62C 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 +97: 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/Chem/rdChemReactions.so +97: 30# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::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 +97: 31# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::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 +97: 32# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::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: 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# 0x00007FEBACDB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +97: 37# 0x00007FEBACDB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +97: 38# 0x00007FEBACDB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +97: 39# 0x00007FEBACDB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +97: 40# 0x00007FEBACDB7933 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# 0x00007FEBAF2183C6 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 +97: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 51# 0x0000000000690C6F in /usr/bin/python3 +97: 52# 0x000000000062D590 in /usr/bin/python3 +97: 53# _PyObject_MakeTpCall in /usr/bin/python3 +97: 54# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 55# 0x00000000005CD3C9 in /usr/bin/python3 +97: 56# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 57# 0x0000000000690C6F in /usr/bin/python3 +97: 58# 0x000000000062D590 in /usr/bin/python3 +97: 59# _PyObject_MakeTpCall in /usr/bin/python3 +97: 60# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 61# 0x00000000005CD3C9 in /usr/bin/python3 +97: 62# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 63# 0x0000000000690C6F in /usr/bin/python3 +97: 64# 0x000000000062D590 in /usr/bin/python3 +97: 65# _PyObject_MakeTpCall in /usr/bin/python3 +97: 66# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 67# 0x00000000005A0A3C in /usr/bin/python3 +97: 68# _PyObject_MakeTpCall in /usr/bin/python3 +97: 69# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 70# PyEval_EvalCode in /usr/bin/python3 +97: 71# 0x00000000006AB8D1 in /usr/bin/python3 +97: 72# 0x00000000006A899C in /usr/bin/python3 +97: 73# 0x00000000006B9943 in /usr/bin/python3 +97: 74# 0x00000000006B93E3 in /usr/bin/python3 +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# 0x00007FEBAFC20CA8 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: +111: processing +111: launch :0 +111: launch :1 +111: launch :2 +111: launch :3 +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: [20:24:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +60: [20:24:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +60: [20:24:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +60: [20:24:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +93: [20:24:13] reactant 0 has no mapped atoms. +93: [20:24:13] product 0 has no mapped atoms. +93: [20:24:13] WARNING: neither stereo atoms nor CIP codes found for double bond. Stereochemistry info will not be propagated to product. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +125: Randomness seeded to: 3898199209 +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 +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. + 89/236 Test #93: testReaction ........................... Passed 0.44 sec + 90/236 Test #99: pyChemReactionSanitize ................. Passed 0.40 sec +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +60: [20:24:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 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: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -97: ........[00:24:57] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])Q -97: [00:24:57] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])Q' for input: '[C:1](=[O:2])Q' -89: [00:24:57] Explicit valence for atom # 4 Al, 6, is greater than permitted -97: [00:24:57] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])[N:3]Q -97: [00:24:57] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])[N:3]Q' for input: '[C:1](=[O:2])[N:3]Q' -97: .[00:24:57] reactant atom-mapping number 1 found multiple times. -97: [00:24:57] product atom-mapping number 2 not found in reactants. -97: [00:24:57] mapped atoms in the reactants were not mapped in the products. -97: unmapped numbers are: 4 -97: [00:24:57] product atom-mapping number 5 not found in reactants. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 88/236 Test #30: pyForceFieldConstraints ................ Passed 0.85 sec -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -75: [00:24:57] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -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 -75: [00:24:57] bond with order 0 found on line 11. This is not part of the MDL specification. -75: [00:24:57] bond with order 0 found on line 16. This is not part of the MDL specification. -67: ..............[00:24:57] SMILES Parse Error: syntax error while parsing: invalidsmiles -67: [00:24:57] SMILES Parse Error: check for mistakes around position 1: -67: [00:24:57] invalidsmiles -67: [00:24:57] ^ -67: [00:24:57] SMILES Parse Error: Failed parsing SMILES 'invalidsmiles' for input: 'invalidsmiles' -98: ..[00:24:57] == testRGroupState -98: .[00:24:57] == testRandomEnumerateAllBBsLibrary +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: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: 200 +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] 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 +97: .........[20:24:13] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +97: [20:24:13] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +97: [20:24:13] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +97: [20:24:13] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +97: .[20:24:13] product atom-mapping number 1 found multiple times. +97: [20:24:13] product atom-mapping number 1 found multiple times. +110: ......... +110: ---------------------------------------------------------------------- +110: Ran 9 tests in 0.067s +110: +110: OK +98: ..[20:24:13] == testRGroupState +98: .[20:24:13] == testRandomEnumerateAllBBsLibrary 98: ** [1, 1] 98: ** [0, 2] 98: ** [1, 0] -129: [00:24:57] ------------------------------------- -129: [00:24:57] Test MHFP fingerprint encoder initialization -89: [00:24:57] Explicit valence for atom # 10 Si, 6, is greater than permitted +116: [20:24:13] done +116: [20:24:13] ------------------------------------- +116: [20:24:13] PBF edge cases. +116: [20:24:13] done 128: 128: 128: @@ -22965,15 +23508,6 @@ 128: 128: ------------------- 128: -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: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -98: .[00:24:57] == testRandomEnumerateLibrary 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 @@ -23121,12 +23655,6 @@ 128: 128: 128: ------------------- -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 -93: [00:24:57] reactant 0 has no mapped atoms. -93: [00:24:57] product 0 has no mapped atoms. -93: [00:24:57] WARNING: neither stereo atoms nor CIP codes found for double bond. Stereochemistry info will not be propagated to product. 128: 128: SMI: n1c[nH]c2cc(O)nc(O)c21 128: Atoms: @@ -23334,532 +23862,104 @@ 128: 128: ------------------- 128: -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: 200 -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -110: ......... -110: ---------------------------------------------------------------------- -110: Ran 9 tests in 0.069s -110: -110: OK -97: [00:24:57] Found a SCD/SED line with missing/empty SDT specification at line 34 -97: [00:24:57] Found a SCD/SED line with missing/empty SDT specification at line 36 -97: [00:24:57] Found a SCD/SED line with missing/empty SDT specification at line 38 -97: [00:24:57] Found a SCD/SED line with missing/empty SDT specification at line 40 -97: [00:24:57] Found a SCD/SED line with missing/empty SDT specification at line 42 -97: [00:24:57] Found a SCD/SED line with missing/empty SDT specification at line 87 -97: [00:24:57] Found a SCD/SED line with missing/empty SDT specification at line 89 -97: [00:24:57] Found a SCD/SED line with missing/empty SDT specification at line 91 -97: [00:24:57] Found a SCD/SED line with missing/empty SDT specification at line 93 -97: [00:24:57] Found a SCD/SED line with missing/empty SDT specification at line 95 -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -98: .[00:24:57] == testRandomSample -129: [00:24:57] done -129: [00:24:57] ------------------------------------- -129: [00:24:57] Test MHFP shingling creation -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [00:24:57] ------------------------------------- -128: [00:24:57] Test Morgan Fingerprints. -98: .[00:24:57] == testRandomSampleAllBBs -128: [00:24:57] done -128: [00:24:57] ------------------------------------- -128: [00:24:57] Test Morgan Fingerprints using fromAtoms argument. -128: [00:24:57] done -128: [00:24:57] ------------------------------------- -128: [00:24:57] Test Morgan Fingerprints as bit vects. -128: [00:24:57] done -128: [00:24:57] ------------------------------------- -128: [00:24:57] Test Morgan Fingerprints with feature invariants. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [00:24:57] done -128: [00:24:57] ------------------------------------- -128: [00:24:57] Test additional Morgan fingerprints options. -128: [00:24:57] done -128: [00:24:57] ------------------------------------- -128: [00:24:57] Test Atom Codes. -128: [00:24:57] done -128: [00:24:57] ------------------------------------- -128: [00:24:57] Test Atom Pairs. -128: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:24:57] done -128: [00:24:57] ------------------------------------- -128: [00:24:57] Test Atom Pairs part 2. -128: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:24:57] done -128: [00:24:57] ------------------------------------- -128: [00:24:57] Test Topological Torsions. -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] done -128: [00:24:57] ------------------------------------- -128: [00:24:57] Test Bulk Topological Torsions. -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -97: ..[00:24:57] SMARTS Parse Error: syntax error while parsing: boromicacid -97: [00:24:57] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' - 89/236 Test #65: testDepictor ........................... Passed 0.71 sec -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -97: [00:24:57] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide -97: [00:24:57] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' -97: [00:24:57] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride -97: [00:24:57] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' -97: [00:24:57] reaction has no reactants -97: [00:24:57] reaction has no products -97: [00:24:57] initialization failed -97: [00:24:57] reaction has no reactants -97: [00:24:57] reaction has no products -97: .[00:24:57] SMARTS Parse Error: syntax error while parsing: boromicacid -97: [00:24:57] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' -97: [00:24:57] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide -97: [00:24:57] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' -97: [00:24:57] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride -97: [00:24:57] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' -97: [00:24:57] reaction has no reactants -97: [00:24:57] reaction has no products -97: [00:24:57] initialization failed -97: [00:24:57] reaction has no reactants -97: [00:24:57] reaction has no products -97: . -97: ---------------------------------------------------------------------- -97: Ran 54 tests in 0.163s -97: -97: OK -97: ******************************************** -97: /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/testData/AmideBond.rxn -97: -98: .[00:24:57] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead -98: [00:24:57] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead -98: .[00:24:57] == testRemoveBadMatches -98: .[00:24:57] == testTimings -116: [00:24:57] done -116: [00:24:57] ------------------------------------- -116: [00:24:57] PBF edge cases. -116: [00:24:57] done -130: [00:24:57] ------------------------------------- -130: [00:24:57] Test atom-pair fp generator -130: [00:24:57] done -130: [00:24:57] ------------------------------------- -130: [00:24:57] Test atom-pair fp generator with different arguments -130: [00:24:57] done -130: [00:24:57] ------------------------------------- -130: [00:24:57] Test compatibility between atom pair implementation for FingerprintGenerator and old atom pairs implementation -130: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -130: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -130: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -130: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -92: Randomness seeded to: 1745830819 -92: =============================================================================== -92: All tests passed (11480 assertions in 38 test cases) -92: -112: [00:24:57] done -112: [00:24:57] ------------------------------------- -112: [00:24:57] Test Github #3806: NaNs from AUTOCORR2D descriptor -112: [00:24:57] done + 91/236 Test #116: testPBF ................................ Passed 0.29 sec +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +98: .[20:24:13] == testRandomEnumerateLibrary +128: [20:24:13] ------------------------------------- +128: [20:24:13] Test Morgan Fingerprints. +128: [20:24:13] done +128: [20:24:13] ------------------------------------- +128: [20:24:13] Test Morgan Fingerprints using fromAtoms argument. +128: [20:24:13] done +128: [20:24:13] ------------------------------------- +128: [20:24:13] Test Morgan Fingerprints as bit vects. +128: [20:24:13] done +128: [20:24:13] ------------------------------------- +128: [20:24:13] Test Morgan Fingerprints with feature invariants. +128: [20:24:13] done +128: [20:24:13] ------------------------------------- +128: [20:24:13] Test additional Morgan fingerprints options. +128: [20:24:13] done +128: [20:24:13] ------------------------------------- +128: [20:24:13] Test Atom Codes. +128: [20:24:13] done +128: [20:24:13] ------------------------------------- +128: [20:24:13] Test Atom Pairs. +128: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [20:24:13] done +128: [20:24:13] ------------------------------------- +128: [20:24:13] Test Atom Pairs part 2. +128: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [20:24:13] done +128: [20:24:13] ------------------------------------- +128: [20:24:13] Test Topological Torsions. +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] done +128: [20:24:13] ------------------------------------- +128: [20:24:13] Test Bulk Topological Torsions. +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +129: [20:24:13] ------------------------------------- +129: [20:24:13] Test MHFP fingerprint encoder initialization 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 - 90/236 Test #75: testMolWriter .......................... Passed 0.63 sec - 91/236 Test #92: testGenericGroups ...................... Passed 0.56 sec - 92/236 Test #112: testAUTOCORR2D ......................... Passed 0.33 sec - 93/236 Test #116: testPBF ................................ Passed 0.31 sec -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -130: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -130: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -130: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -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 -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 -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 -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 -129: [00:24:57] done -129: [00:24:57] ------------------------------------- -129: [00:24:57] Test MHFP hashing of string and uint arrays -129: [00:24:57] done -129: [00:24:57] ------------------------------------- -129: [00:24:57] Test SECFP fingerprint functionality -129: [00:24:57] done - 94/236 Test #110: pyFragCatalog .......................... Passed 0.42 sec - 95/236 Test #93: testReaction ........................... Passed 0.62 sec -125: Randomness seeded to: 2069922146 -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 -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -130: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -130: [00:24:57] done -130: [00:24:57] ------------------------------------- -130: [00:24:57] Test atom-pair additional output -130: [00:24:57] done -130: [00:24:57] ------------------------------------- -130: [00:24:57] Test Folded Atom Pairs. -130: [00:24:57] done -130: [00:24:57] ------------------------------------- -130: [00:24:57] Test Rooted Atom Pairs. -130: [00:24:57] done -130: [00:24:57] ------------------------------------- -130: [00:24:57] Test ignoring atoms in Atom Pairs. -130: [00:24:57] done -130: [00:24:57] ------------------------------------- -130: [00:24:57] Test Atom Pairs including info about chirality. -130: [00:24:57] done -130: [00:24:57] ------------------------------------- -130: [00:24:57] Test Morgan Fingerprints. -130: [00:24:57] done -130: [00:24:57] ------------------------------------- -130: [00:24:57] Test morgan fp generator -130: [00:24:57] done -130: [00:24:57] ------------------------------------- -130: [00:24:57] Test Morgan Fingerprints using fromAtoms argument. -130: [00:24:57] done -130: [00:24:57] ------------------------------------- -130: [00:24:57] Test Morgan Fingerprints as bit vects. -130: [00:24:57] done -130: [00:24:57] ------------------------------------- -130: [00:24:57] Test Morgan Fingerprints with feature invariants. -130: [00:24:57] done -130: [00:24:57] ------------------------------------- -130: [00:24:57] Test additional Morgan fingerprints options. -130: [00:24:57] done -130: [00:24:57] ------------------------------------- -130: [00:24:57] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints -130: [00:24:57] done -130: [00:24:57] ------------------------------------- -130: [00:24:57] Single atoms setting radius 1 bits in Morgan fingerprints -130: [00:24:57] done -130: [00:24:57] ------------------------------------- -130: [00:24:57] Test different invariant generator combinations -130: [00:24:57] done -130: [00:24:57] ------------------------------------- -130: [00:24:57] Test invariant overriding -130: [00:24:57] done -130: [00:24:57] ------------------------------------- -130: [00:24:57] Test RDKit fp generator -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 -35: [00:24:57] 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 -35: [00:24:57] ----------------------- -35: Testing isRingFused -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: +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +97: ................[20:24:13] mapped atoms in the reactants were not mapped in the products. +97: unmapped numbers are: 3 +97: [20:24:13] 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. +98: .[20:24:13] == testRandomSample +98: .[20:24:13] == testRandomSampleAllBBs +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator 68: Test 68: -68: FalseChiral.mrv +68: marvin03.mrv 68: 68: Test 68: @@ -23867,876 +23967,915 @@ 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: FalseAtropisomer.mrv 68: 68: Test 68: -68: data_sgroup_empty_field_data.mrv +68: AtropEnhancedStereo.mrv 68: 68: Test 68: -68: radical_value.mrv +68: AtropManyChirals.mrv 68: 68: Test 68: -68: emptyOneLineAtomList.mrv +68: AtropManyChiralsEnhanced.mrv 68: 68: Test 68: -68: mrvValence_value.mrv +68: AtropManyChiralsEnhanced2.mrv 68: 68: Test 68: -68: ChiralTest2.mrv +68: AtropManyChiralsEnhanced3.mrv 68: 68: Test 68: -68: ChiralTest.mrv +68: AtropManyChiralsEnhanced4.mrv 68: 68: Test 68: -68: SnCl2.mrv +68: BMS-986142_3d_chiral.mrv 68: 68: Test 68: -68: SnH2Cl2.mrv +68: BMS-986142_3d.mrv 68: 68: Test 68: -68: marvin01.mrv +68: BMS-986142_atrop1.mrv 68: 68: Test 68: -68: marvin02.mrv +68: BMS-986142_atrop2.mrv 68: 68: Test 68: -68: marvin07.mrv +68: BMS-986142_atrop3.mrv 68: 68: Test 68: -68: marvin10.mrv +68: BMS-986142_atrop4.mrv 68: 68: Test 68: -68: marvin06.mrv +68: BMS-986142_atrop5.mrv 68: +68: [20:24:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +68: [20:24:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +98: .[20:24:13] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead +30: ... +30: ---------------------------------------------------------------------- +30: Ran 12 tests in 0.544s +30: +30: OK +129: [20:24:13] done +129: [20:24:13] ------------------------------------- +129: [20:24:13] Test MHFP shingling creation +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +98: [20:24:13] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead +98: .[20:24:13] == testRemoveBadMatches +98: .[20:24:13] == testTimings +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +97: [20:24:13] mapped atoms in the reactants were not mapped in the products. +97: unmapped numbers are: 3 +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +130: [20:24:13] ------------------------------------- +130: [20:24:13] Test atom-pair fp generator +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +97: ..[20:24:13] reactant 2 has no mapped atoms. +97: [20:24:13] reactant 2 has no mapped atoms. +97: [20:24:13] product 1 has no mapped atoms. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +129: [20:24:13] done +129: [20:24:13] ------------------------------------- +129: [20:24:13] Test MHFP hashing of string and uint arrays +129: [20:24:13] done +129: [20:24:13] ------------------------------------- +129: [20:24:13] Test SECFP fingerprint functionality 68: Test 68: -68: marvin12.mrv +68: BMS-986142_atrop6.mrv 68: 68: Test 68: -68: EmptyMol.mrv +68: BMS-986142_atrop7.mrv 68: 68: Test 68: -68: Sparse.mrv +68: BMS-986142_atrop8.mrv 68: +68: [20:24:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +68: [20:24:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored + 92/236 Test #110: pyFragCatalog .......................... Passed 0.39 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 +97: ........[20:24:13] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])Q +97: [20:24:13] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])Q' for input: '[C:1](=[O:2])Q' +97: [20:24:13] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])[N:3]Q +97: [20:24:13] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])[N:3]Q' for input: '[C:1](=[O:2])[N:3]Q' +97: .[20:24:13] reactant atom-mapping number 1 found multiple times. +97: [20:24:13] product atom-mapping number 2 not found in reactants. +97: [20:24:13] mapped atoms in the reactants were not mapped in the products. +97: unmapped numbers are: 4 +97: [20:24:13] product atom-mapping number 5 not found in reactants. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +131: Randomness seeded to: 2000038310 +131: =============================================================================== +131: All tests passed (188 assertions in 16 test cases) +131: +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator 68: Test 68: -68: Sparse2.mrv +68: BMS-986142_atropBad2.mrv 68: +68: [20:24:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +130: [20:24:13] done +130: [20:24:13] ------------------------------------- +130: [20:24:13] Test atom-pair fp generator with different arguments +130: [20:24:13] done +130: [20:24:13] ------------------------------------- +130: [20:24:13] Test compatibility between atom pair implementation for FingerprintGenerator and old atom pairs implementation +130: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +130: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +130: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +130: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +130: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +130: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +130: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +125: Warning: Atom Count for residue GLU5A does not match expected count +129: [20:24:13] done + 93/236 Test #131: fpTestCatch ............................ Passed 0.04 sec + 94/236 Test #129: testMHFPFingerprint .................... Passed 0.09 sec +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 +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 +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +130: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +130: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +130: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +67: ..... +67: ---------------------------------------------------------------------- +67: Ran 19 tests in 0.453s +67: +67: OK +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +92: Randomness seeded to: 405069 +92: =============================================================================== +92: All tests passed (11480 assertions in 38 test cases) +92: +89: [20:24:13] Explicit valence for atom # 9 N, 5, is greater than permitted +120: [20:24:13] done +120: [20:24:13] ------------------------------------- +120: [20:24:13] More PMI/NPR tests. +120: [20:24:13] done +120: [20:24:13] ------------------------------------- +120: [20:24:13] Basic NPR tests. + 95/236 Test #92: testGenericGroups ...................... Passed 0.56 sec +130: [20:24:13] done +130: [20:24:13] ------------------------------------- +130: [20:24:13] Test atom-pair additional output +130: [20:24:13] done +130: [20:24:13] ------------------------------------- +130: [20:24:13] Test Folded Atom Pairs. +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 +130: [20:24:13] done +130: [20:24:13] ------------------------------------- +130: [20:24:13] Test Rooted Atom Pairs. +130: [20:24:13] done +130: [20:24:13] ------------------------------------- +130: [20:24:13] Test ignoring atoms in Atom Pairs. +130: [20:24:13] done +130: [20:24:13] ------------------------------------- +130: [20:24:13] Test Atom Pairs including info about chirality. +130: [20:24:13] done +130: [20:24:13] ------------------------------------- +130: [20:24:13] Test Morgan Fingerprints. +130: [20:24:13] done +130: [20:24:13] ------------------------------------- +130: [20:24:13] Test morgan fp generator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator 68: Test 68: -68: Sparse3.mrv +68: JDQ443_3d.mrv 68: 68: Test 68: -68: MarvinNoCoords.mrv +68: JDQ443_atrop1.mrv 68: 68: Test 68: -68: aspirin.mrv +68: JDQ443_atrop2.mrv 68: 68: Test 68: -68: MarvinStereoGroupsZeros.mrv +68: JDQ443_atrop3.mrv 68: 68: Test 68: -68: MarvinStereoGroupsAbs.mrv +68: JDQ443_atropBad1.mrv 68: +68: [20:24:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: 300 +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +130: [20:24:13] done +130: [20:24:13] ------------------------------------- +130: [20:24:13] Test Morgan Fingerprints using fromAtoms argument. +130: [20:24:13] done +130: [20:24:13] ------------------------------------- +130: [20:24:13] Test Morgan Fingerprints as bit vects. +130: [20:24:13] done +130: [20:24:13] ------------------------------------- +130: [20:24:13] Test Morgan Fingerprints with feature invariants. +130: [20:24:13] done +130: [20:24:13] ------------------------------------- +130: [20:24:13] Test additional Morgan fingerprints options. +130: [20:24:13] done +130: [20:24:13] ------------------------------------- +130: [20:24:13] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints +130: [20:24:13] done +130: [20:24:13] ------------------------------------- +130: [20:24:13] Single atoms setting radius 1 bits in Morgan fingerprints 68: Test 68: -68: triphenylphosphine.mrv +68: RP-6306_atrop1.mrv 68: 68: Test 68: -68: MarvinOldSuperGroupTest.mrv +68: RP-6306_atrop2.mrv 68: 68: Test 68: -68: RadicalTests.mrv +68: RP-6306_atrop3.mrv 68: 68: Test 68: -68: AnyBond.mrv +68: RP-6306_atrop4.mrv 68: 68: Test 68: -68: cisBenzene.mrv +68: RP-6306_atrop5.mrv 68: +68: [20:24:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +68: [20:24:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator 68: Test 68: -68: DativeBond.mrv +68: RP-6306_atropBad1.mrv 68: +68: [20:24:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +130: [20:24:13] done +130: [20:24:13] ------------------------------------- +130: [20:24:13] Test different invariant generator combinations +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [20:24:13] done +130: [20:24:13] ------------------------------------- +130: [20:24:13] Test invariant overriding +130: [20:24:13] done +130: [20:24:13] ------------------------------------- +130: [20:24:13] Test RDKit fp generator +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 68: Test 68: -68: MultipleSgroup.mrv +68: RP-6306_atropBad2.mrv 68: +68: [20:24:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +68: [20:24:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +68: [20:24:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 + 96/236 Test #67: pyDepictor ............................. Passed 0.78 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 + 97/236 Test #135: testPartialCharges ..................... Passed 0.04 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: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +112: [20:24:13] done +112: [20:24:13] ------------------------------------- +112: [20:24:13] Test Github #3806: NaNs from AUTOCORR2D descriptor +112: [20:24:13] done + 98/236 Test #112: testAUTOCORR2D ......................... Passed 0.46 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 +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 +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] 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: [20:24:13] test on : 365 molecules done +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +97: [20:24:13] Found a SCD/SED line with missing/empty SDT specification at line 34 +97: [20:24:13] Found a SCD/SED line with missing/empty SDT specification at line 36 +97: [20:24:13] Found a SCD/SED line with missing/empty SDT specification at line 38 +97: [20:24:13] Found a SCD/SED line with missing/empty SDT specification at line 40 +97: [20:24:13] Found a SCD/SED line with missing/empty SDT specification at line 42 +97: [20:24:13] Found a SCD/SED line with missing/empty SDT specification at line 87 +97: [20:24:13] Found a SCD/SED line with missing/empty SDT specification at line 89 +97: [20:24:13] Found a SCD/SED line with missing/empty SDT specification at line 91 +97: [20:24:13] Found a SCD/SED line with missing/empty SDT specification at line 93 +97: [20:24:13] Found a SCD/SED line with missing/empty SDT specification at line 95 68: Test 68: -68: SgroupExpanded.mrv +68: RP-6306_3d.mrv 68: 68: Test 68: -68: SgroupMultAttach.mrv +68: Sotorasib_atrop1.mrv 68: 68: Test 68: -68: MarvinMissingX2.mrv +68: Sotorasib_atrop2.mrv 68: 68: Test 68: -68: MarvinMissingY2.mrv +68: Sotorasib_atrop3.mrv 68: 68: Test 68: -68: DataSgroup.mrv +68: Sotorasib_atrop4.mrv 68: 68: Test 68: -68: MulticenterSgroup.mrv +68: Sotorasib_atrop5.mrv 68: -68: [00:24:57] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -68: [00:24:57] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -131: Randomness seeded to: 1553102761 -131: =============================================================================== -131: All tests passed (188 assertions in 16 test cases) -131: - 96/236 Test #97: pyChemReactions ........................ Passed 0.60 sec - 97/236 Test #129: testMHFPFingerprint .................... Passed 0.19 sec - 98/236 Test #131: fpTestCatch ............................ Passed 0.11 sec - 99/236 Test #135: testPartialCharges ..................... Passed 0.09 sec -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: 300 -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] 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 +68: [20:24:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +68: [20:24:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored + 99/236 Test #121: testWHIM ............................... Passed 0.38 sec +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 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: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] done +128: [20:24:13] ------------------------------------- +128: [20:24:13] Test Hashed Atom Pairs. +128: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [20:24:13] done +128: [20:24:13] ------------------------------------- +128: [20:24:13] Test Hashed torsions. +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] done +128: [20:24:13] ------------------------------------- +128: [20:24:13] Test Rooted Atom Pairs. +128: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [20:24:13] done +128: [20:24:13] ------------------------------------- +128: [20:24:13] Test ignoring atoms in Atom Pairs. +128: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [20:24:13] done +128: [20:24:13] ------------------------------------- +128: [20:24:13] Test Rooted Topological Torsions. +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] done +128: [20:24:13] ------------------------------------- +128: [20:24:13] Test ignoring atoms in Topological Torsions. +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] done +128: [20:24:13] ------------------------------------- +128: [20:24:13] Test atom info from morgan fingerprints. +128: [20:24:13] done +128: [20:24:13] ------------------------------------- +128: [20:24:13] Test atom info from morgan fingerprints including Info Redundant Environments. +128: [20:24:13] done +128: [20:24:13] ------------------------------------- +128: [20:24:13] ------------------------------------- +128: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +68: Test +68: +68: Sotorasib_atropBad1.mrv +68: +68: [20:24:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +100/236 Test #30: pyForceFieldConstraints ................ Passed 0.94 sec +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 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: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] 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: [20:24:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] ------------------------------------- +128: [20:24:13] ------------------------------------- +128: [20:24:13] ------------------------------------- +128: [20:24:13] ------------------------------------- +128: [20:24:13] Test Atom Pairs including info about chirality. +128: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [20:24:13] done +128: [20:24:13] ------------------------------------- +128: [20:24:13] Test Topological Torsions including info about chirality. +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] done +128: [20:24:13] ------------------------------------- +128: [20:24:13] Test GitHub Issue 25: fingerprint backwards compatibility. +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [20:24:13] done +128: [20:24:13] ------------------------------------- +128: [20:24:13] Test GitHub Issue 151: PatternFingerprint problems +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +97: ..[20:24:13] SMARTS Parse Error: syntax error while parsing: boromicacid +97: [20:24:13] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +128: [20:24:13] done +128: [20:24:13] ------------------------------------- +128: [20:24:13] Test 3D atom pairs. +128: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [20:24:13] done +128: [20:24:13] ------------------------------------- +128: [20:24:13] Test GitHub Issue 195: GenMACCSKeys() raises an exception with an empty molecule +128: [20:24:13] done +128: [20:24:13] ------------------------------------- +128: [20:24:13] Test multithreading with the pattern FP +128: reading molecules +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +97: [20:24:13] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide +97: [20:24:13] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +138: Randomness seeded to: 548161117 +138: =============================================================================== +138: All tests passed (4 assertions in 1 test case) +138: +101/236 Test #138: molTransformsTestCatch ................. Passed 0.05 sec +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 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 -100/236 Test #35: graphmolMolOpsTest ..................... Passed 1.09 sec -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: [00:24:57] -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# 0x000055834170B99F in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol -68: 3# 0x000055834171669C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol -68: 4# 0x0000558341703A5D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol -68: 5# 0x00007F61B4C33CA8 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# 0x0000558341703BE1 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 -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 -68: Test -68: -68: MarvinBadStereoGroupsAbs.mrv -68: -68: Unrecognized group definition -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 -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 -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: 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 -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 -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: +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +97: [20:24:13] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride +97: [20:24:13] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' +97: [20:24:13] reaction has no reactants +97: [20:24:13] reaction has no products +97: [20:24:13] initialization failed +97: [20:24:13] reaction has no reactants +97: [20:24:13] reaction has no products +97: .[20:24:13] SMARTS Parse Error: syntax error while parsing: boromicacid +97: [20:24:13] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' 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: Sotorasib_3d.mrv 68: 68: Test 68: -68: BMS-986142_atrop2.mrv +68: ZM374979_atrop1.mrv 68: 68: Test 68: -68: BMS-986142_atrop3.mrv +68: ZM374979_atrop2.mrv 68: 68: Test 68: -68: BMS-986142_atrop4.mrv +68: ZM374979_atrop3.mrv 68: 68: Test 68: -68: BMS-986142_atrop5.mrv +68: ZM374979_atropBad1.mrv 68: -68: [00:24:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -68: [00:24:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -67: ..... -67: ---------------------------------------------------------------------- -67: Ran 19 tests in 0.477s -67: -67: OK -69: [00:24:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -69: [00:24:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -69: [00:24:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -69: [00:24:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -69: [00:24:57] deprecated group abbreviation ignored on line 24 -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: [00:24:57] -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# 0x00007F4415CC8531 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 4# 0x00007F4415CD1DFA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 5# 0x00007F4415CD217D 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# 0x0000563C49678C15 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 10# 0x0000563C496DF372 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 11# 0x0000563C4965F923 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 12# 0x00007F4415233CA8 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# 0x0000563C4965FAD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: ---------- -69: **** -69: -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] done -128: [00:24:57] ------------------------------------- -128: [00:24:57] Test Hashed Atom Pairs. -128: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:24:57] done -128: [00:24:57] ------------------------------------- -128: [00:24:57] Test Hashed torsions. -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] done -128: [00:24:57] ------------------------------------- -128: [00:24:57] Test Rooted Atom Pairs. -128: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:24:57] done -128: [00:24:57] ------------------------------------- -128: [00:24:57] Test ignoring atoms in Atom Pairs. -128: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:24:57] done -128: [00:24:57] ------------------------------------- -128: [00:24:57] Test Rooted Topological Torsions. -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] done -128: [00:24:57] ------------------------------------- -128: [00:24:57] Test ignoring atoms in Topological Torsions. -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] done -128: [00:24:57] ------------------------------------- -128: [00:24:57] Test atom info from morgan fingerprints. -128: [00:24:57] done -128: [00:24:57] ------------------------------------- -128: [00:24:57] Test atom info from morgan fingerprints including Info Redundant Environments. -128: [00:24:57] done -128: [00:24:57] ------------------------------------- -128: [00:24:57] ------------------------------------- -128: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] ------------------------------------- -128: [00:24:57] ------------------------------------- -128: [00:24:57] ------------------------------------- -128: [00:24:57] ------------------------------------- -128: [00:24:57] Test Atom Pairs including info about chirality. -128: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:24:57] done -128: [00:24:57] ------------------------------------- -128: [00:24:57] Test Topological Torsions including info about chirality. -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] done -128: [00:24:57] ------------------------------------- -128: [00:24:57] Test GitHub Issue 25: fingerprint backwards compatibility. -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:24:57] done -128: [00:24:57] ------------------------------------- -128: [00:24:57] Test GitHub Issue 151: PatternFingerprint problems -128: [00:24:57] done -128: [00:24:57] ------------------------------------- -128: [00:24:57] Test 3D atom pairs. -128: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:24:57] done -128: [00:24:57] ------------------------------------- -128: [00:24:57] Test GitHub Issue 195: GenMACCSKeys() raises an exception with an empty molecule -128: [00:24:57] done -128: [00:24:57] ------------------------------------- -128: [00:24:57] Test multithreading with the pattern FP -128: reading molecules -128: pass 1 -128: launch :0 -128: launch :1 -128: launch :2 -128: launch :3 -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 -89: [00:24:57] Explicit valence for atom # 2 O, 4, is greater than permitted -89: [00:24:57] Explicit valence for atom # 3 Be, 4, is greater than permitted -89: [00:24:57] Explicit valence for atom # 3 Al, 6, is greater than permitted -89: [00:24:57] Explicit valence for atom # 27 P, 6, is greater than permitted -125: Warning: Atom Count for residue GLU5A does not match expected count -132: Randomness seeded to: 922413990 -132: =============================================================================== -132: All tests passed (2737 assertions in 7 test cases) -132: -121: =>start test WHIM -121: [00:24:57] test on : 365 molecules done +68: [20:24:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +89: [20:24:13] Explicit valence for atom # 3 Al, 6, is greater than permitted +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +97: [20:24:13] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide +97: [20:24:13] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' +97: [20:24:13] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride +97: [20:24:13] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' +97: [20:24:13] reaction has no reactants +97: [20:24:13] reaction has no products +97: [20:24:13] initialization failed +97: [20:24:13] reaction has no reactants +97: [20:24:13] reaction has no products +97: . +97: ---------------------------------------------------------------------- +97: Ran 54 tests in 0.311s +97: +97: OK +140: Randomness seeded to: 2468283328 +140: =============================================================================== +140: All tests passed (17 assertions in 2 test cases) +140: +97: ******************************************** +97: /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/testData/AmideBond.rxn +97: +102/236 Test #140: forceFieldHelpersCatch ................. Passed 0.05 sec 137: *********************************************************** 137: Testing MolTransforms 137: --------------------------------- @@ -24767,53 +24906,45 @@ 137: testWeightedCentroid 137: 137: *********************************************************** -114: [00:24:57] ------------------------------------- -114: [00:24:57] Test empty molecule BCUT. -117: =>start test rdf custom -117: [00:24:57] test on : 365 molecules done -138: Randomness seeded to: 531839953 -138: =============================================================================== -138: All tests passed (4 assertions in 1 test case) -138: -101/236 Test #67: pyDepictor ............................. Passed 0.86 sec -102/236 Test #114: testBCUT ............................... Passed 0.55 sec -103/236 Test #121: testWHIM ............................... Passed 0.51 sec -104/236 Test #132: fpGenTestCatch ......................... Passed 0.23 sec -105/236 Test #137: testMolTransforms ...................... Passed 0.16 sec -106/236 Test #138: molTransformsTestCatch ................. Passed 0.13 sec -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +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 +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: 400 -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +128: pass 1 +128: launch :0 +128: launch :1 +128: launch :2 +128: launch :3 +141: [20:24:13] ------------------------------------- +141: [20:24:13] Test MMFF atom types. +132: Randomness seeded to: 1618712184 +132: =============================================================================== +132: All tests passed (2737 assertions in 7 test cases) +132: +103/236 Test #132: fpGenTestCatch ......................... Passed 0.18 sec +104/236 Test #137: testMolTransforms ...................... Passed 0.10 sec +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +141: [20:24:13] done +141: [20:24:13] ------------------------------------- +141: [20:24:13] Testing MMFF builder tools. +35: [20:24:13] Maximum BFS search size exceeded. +35: This is likely due to a highly symmetric fused ring system. test 143 Start 143: testUFFForceFieldHelpers @@ -24826,443 +24957,528 @@ 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: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +141: [20:24:13] done +141: [20:24:13] ------------------------------------- +141: [20:24:13] Testing MMFF builder+minimization. +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: [20:24:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +142: [20:24:13] ------------------------------------- +142: [20:24:13] Test MMFF multithreading +117: =>start test rdf custom +117: [20:24:13] test on : 365 molecules done +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +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 +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +144: ------------------------------------- +144: Test CrystalFF torsional term. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +143: [20:24:13] ------------------------------------- +143: [20:24:13] Test UFF atom labels. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] 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: [20:24:13] test on : 365 molecules done +35: [20:24:13] ----------------------- +35: Testing isRingFused +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +105/236 Test #123: testAUTOCORR3D ......................... Passed 0.46 sec 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: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +143: [20:24:13] done +143: [20:24:13] ------------------------------------- +143: [20:24:13] Test UFF atom typer. +143: [20:24:13] done +143: [20:24:13] ------------------------------------- +143: [20:24:13] Testing UFF builder tools. +143: [20:24:13] done +143: [20:24:13] ------------------------------------- +143: [20:24:13] Testing UFF builder+minimization. +89: [20:24:13] Explicit valence for atom # 4 Al, 6, is greater than permitted +141: [20:24:13] done +141: [20:24:13] ------------------------------------- +141: [20:24:13] Testing Issue239. +106/236 Test #35: graphmolMolOpsTest ..................... Passed 1.07 sec +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 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 +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +114: [20:24:13] ------------------------------------- +114: [20:24:13] Test empty molecule BCUT. +107/236 Test #114: testBCUT ............................... Passed 0.61 sec 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: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] 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 +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 +142: launch :18 +142: launch :19 +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +108/236 Test #97: pyChemReactions ........................ Passed 0.79 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: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +141: [20:24:13] done +141: [20:24:13] ------------------------------------- +141: [20:24:13] Testing calcEnergy with passed coords. +142: launch :20 +142: launch :21 +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +147: Randomness seeded to: 685251701 +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +89: [20:24:13] Explicit valence for atom # 10 Si, 6, is greater than permitted +141: [20:24:13] done +141: [20:24:13] ------------------------------------- +141: [20:24:13] Testing calcGrad. +146: [20:24:13] ******************************************************** +146: [20:24:13] Testing DistGeomHelpers +146: [20:24:13] --------------------------------- +146: [20:24:13] test2 +146: +146: go +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: Elapsed time: 0.620037 s +115: Errors:0 +115: [20:24:13] test on : 500 molecules done +125: Warning: Atom Count for residue ASN39A does not match expected count +120: [20:24:13] done +120: [20:24:13] ------------------------------------- +120: [20:24:13] PMI edge cases. +120: [20:24:13] done +120: [20:24:13] ------------------------------------- +120: [20:24:13] NPR edge cases. +120: [20:24:13] done +120: [20:24:13] ------------------------------------- +120: [20:24:13] 3D descriptors. +120: [20:24:13] done +120: [20:24:13] ------------------------------------- +120: [20:24:13] 3D descriptor edge cases. +120: [20:24:13] done +120: [20:24:13] ------------------------------------- +120: [20:24:13] Inertial shape factor. +120: [20:24:13] done +109/236 Test #115: testEEM ................................ Passed 0.65 sec +110/236 Test #120: test3D ................................. Passed 0.58 sec +146: ------------------------------------- +146: +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 +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 +142: launch :22 +142: launch :23 +141: [20:24:13] done +141: [20:24:13] ------------------------------------- +141: [20:24:13] Testing Issue242. 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: FalseAtropisomer.mrv 68: -68: [00:24:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -68: [00:24:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 68: Test 68: -68: BMS-986142_atropBad2.mrv +68: AtropEnhancedStereo.mrv 68: -68: [00:24:57] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 68: Test 68: -68: JDQ443_3d.mrv +68: AtropManyChirals.mrv 68: 68: Test 68: -68: JDQ443_atrop1.mrv +68: AtropManyChiralsEnhanced.mrv 68: 68: Test 68: -68: JDQ443_atrop2.mrv +68: AtropManyChiralsEnhanced2.mrv 68: 68: Test 68: -68: JDQ443_atrop3.mrv +68: AtropManyChiralsEnhanced3.mrv 68: 68: Test 68: -68: JDQ443_atropBad1.mrv +68: AtropManyChiralsEnhanced4.mrv 68: -68: [00:24:57] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 68: Test 68: -68: RP-6306_atrop1.mrv +68: BMS-986142_3d_chiral.mrv 68: 68: Test 68: -68: RP-6306_atrop2.mrv +68: BMS-986142_3d.mrv 68: 68: Test 68: -68: RP-6306_atrop3.mrv +68: BMS-986142_atrop1.mrv 68: 68: Test 68: -68: RP-6306_atrop4.mrv +68: BMS-986142_atrop2.mrv 68: 68: Test 68: -68: RP-6306_atrop5.mrv +68: BMS-986142_atrop3.mrv 68: -68: [00:24:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -68: [00:24:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -141: [00:24:57] ------------------------------------- -141: [00:24:57] Test MMFF atom types. -141: [00:24:57] done -141: [00:24:57] ------------------------------------- -141: [00:24:57] Testing MMFF builder tools. -141: [00:24:57] done -141: [00:24:57] ------------------------------------- -141: [00:24:57] Testing MMFF builder+minimization. -123: =>start test autocorr3D -123: [00:24:57] test on : 365 molecules done -107/236 Test #123: testAUTOCORR3D ......................... Passed 0.45 sec -120: [00:24:57] done -120: [00:24:57] ------------------------------------- -120: [00:24:57] More PMI/NPR tests. -120: [00:24:57] done -120: [00:24:57] ------------------------------------- -120: [00:24:57] Basic NPR tests. -140: Randomness seeded to: 442900671 -140: =============================================================================== -140: All tests passed (17 assertions in 2 test cases) -140: -142: [00:24:57] ------------------------------------- -142: [00:24:57] Test MMFF multithreading -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -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: RP-6306_atropBad1.mrv +68: BMS-986142_atrop4.mrv 68: -68: [00:24:57] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 68: Test 68: -68: RP-6306_atropBad2.mrv +68: BMS-986142_atrop5.mrv 68: -68: [00:24:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -68: [00:24:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -68: [00:24:57] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -108/236 Test #140: forceFieldHelpersCatch ................. Passed 0.11 sec -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] 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 -144: ------------------------------------- -144: Test CrystalFF torsional term. -143: [00:24:57] ------------------------------------- -143: [00:24:57] Test UFF atom labels. -141: [00:24:57] done -141: [00:24:57] ------------------------------------- -141: [00:24:57] Testing Issue239. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: [00:24:57] 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: [00:24:57] 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: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +68: [20:24:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +68: [20:24:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +126: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +126: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +126: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +126: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +126: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +126: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +126: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +126: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +126: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +126: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +126: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +126: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +126: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +147: [20:24:13] [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: [20:24:13] [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)] 118: =>start test rdf -118: [00:24:57] test on : 365 molecules done -109/236 Test #118: testRDF ................................ Passed 0.59 sec -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +118: [20:24:13] test on : 365 molecules done +141: [20:24:13] done +141: [20:24:13] ------------------------------------- +141: [20:24:13] Testing github 308: crash during MMFF parameterization . +141: [20:24:13] ------------------------------------- +141: [20:24:13] Testing SFIssue1653802. +126: ..[20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +126: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +126: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +126: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +126: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +126: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +126: .[20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +126: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +126: [20:24:13] DEPRECATION WARNING: please use AtomPairGenerator +111/236 Test #118: testRDF ................................ Passed 0.66 sec +141: [20:24:13] done +141: [20:24:13] ------------------------------------- +141: [20:24:13] Testing SFIssue2378119. +141: [20:24:13] done +141: [20:24:13] ------------------------------------- +141: [20:24:13] Test MMFF force-field parameter getters. 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: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [00:24:57] done -143: [00:24:57] ------------------------------------- -143: [00:24:57] Test UFF atom typer. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [00:24:57] done -143: [00:24:57] ------------------------------------- -143: [00:24:57] Testing UFF builder tools. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +141: [20:24:13] ------------------------------------- +141: [20:24:13] Test MMFF multithreading +141: generating reference data +147: [20:24:13] [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: [20:24:13] [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: [20:24:13] [!#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: [20:24:13] [!#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: [20:24:13] [!#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: [20:24:13] [!#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: [20:24:13] [!#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: [20:24:13] [!#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: [20:24:13] [!#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: [20:24:13] [!#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: [20:24:13] [!#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: [20:24:13] [!#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: [20:24:13] [!#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: [20:24:13] [!#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: [20:24:13] [!#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: [20:24:13] [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: [20:24:13] [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: [20:24:13] [*: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: [20:24:13] [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: [20:24:13] [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: [20:24:13] [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: [20:24:13] [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: [20:24:13] [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: [20:24:13] [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: [20:24:13] [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: [20:24:13] [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: [20:24:13] [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: [20:24:13] [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: [20:24:13] [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: [20:24:13] [$([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: [20:24:13] [$(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: [20:24:13] [$(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: [20:24:13] [$(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: [20:24:13] [$(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: [20:24:13] [$(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: [20:24:13] [$(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: [20:24:13] [$(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: [20:24:13] [$(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)] +147: [20:24:13] [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: [20:24:13] [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: [20:24:13] [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: [20:24:13] [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: [20:24:13] [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: [20:24:13] 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: [20:24:13] [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: [20:24:13] [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: [20:24:13] [!#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: [20:24:13] [!#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: [20:24:13] [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: [20:24:13] [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: [20:24:13] [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: [20:24:13] [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: [20:24:13] [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: [20:24:13] [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: [20:24:13] [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: [20:24:13] [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)] +147: ----------- 134: .. 134: ---------------------------------------------------------------------- 134: Ran 2 tests in 0.038s 134: 134: OK -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -141: [00:24:57] done -141: [00:24:57] ------------------------------------- -141: [00:24:57] Testing calcEnergy with passed coords. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -147: Randomness seeded to: 4037749009 -115: [00:24:57] 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: BMS-986142_atrop6.mrv 68: 68: Test 68: -68: Sotorasib_atrop4.mrv +68: BMS-986142_atrop7.mrv 68: 68: Test 68: -68: Sotorasib_atrop5.mrv +68: BMS-986142_atrop8.mrv 68: -68: [00:24:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -68: [00:24:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [00:24:57] done -143: [00:24:57] ------------------------------------- -143: [00:24:57] Testing UFF builder+minimization. -130: [00:24:57] done -130: [00:24:57] ------------------------------------- -130: [00:24:57] Test unfolded version of RDKFP -130: [00:24:57] ------------------------------------- -130: [00:24:57] Test topological torsion fp generator -130: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -130: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -130: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -130: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -146: [00:24:57] ******************************************************** -146: [00:24:57] Testing DistGeomHelpers -146: [00:24:57] --------------------------------- -146: [00:24:57] test2 -146: -146: go -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -141: [00:24:57] done -141: [00:24:57] ------------------------------------- -141: [00:24:57] Testing calcGrad. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -130: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -146: ------------------------------------- -146: -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -130: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [00:24:57] done -130: [00:24:57] ------------------------------------- -130: [00:24:57] Test Topological Torsions. -130: [00:24:57] done -130: [00:24:57] ------------------------------------- -130: [00:24:57] Test Folded torsions. -130: [00:24:57] done -130: [00:24:57] ------------------------------------- -130: [00:24:57] Test Bulk Topological Torsions. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: pass 2 -128: launch :0 -128: launch :1 -128: launch :2 -128: launch :3 -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] 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 -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -142: launch :3 -142: launch :4 -142: launch :5 -142: launch :6 -142: launch :7 -142: launch :8 -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -142: launch :9 -142: launch :10 -141: [00:24:57] done -141: [00:24:57] ------------------------------------- -141: [00:24:57] Testing Issue242. -142: launch :11 -142: launch :12 -142: launch :13 -142: launch :14 -142: launch :15 -142: launch :16 -142: launch :17 -142: launch :18 -142: launch :19 -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -142: launch :20 -110/236 Test #134: pyTestMHFP ............................. Passed 0.33 sec -142: launch :21 -142: launch :22 -142: launch :23 -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: Elapsed time: 0.639639 s -115: Errors:0 -115: [00:24:57] test on : 500 molecules done -147: [00:24:57] [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: [00:24:57] [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)] -147: [00:24:57] [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: [00:24:57] [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: [00:24:57] [!#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: [00:24:57] [!#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: [00:24:57] [!#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: [00:24:57] [!#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: [00:24:57] [!#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: [00:24:57] [!#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: [00:24:57] [!#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: [00:24:57] [!#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: [00:24:57] [!#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: [00:24:57] [!#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: [00:24:57] [!#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: [00:24:57] [!#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: [00:24:57] [!#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: [00:24:57] [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: [00:24:57] [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: [00:24:57] [*: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: [00:24:57] [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: [00:24:57] [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: [00:24:57] [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: [00:24:57] [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: [00:24:57] [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: [00:24:57] [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: [00:24:57] [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: [00:24:57] [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: [00:24:57] [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: [00:24:57] [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: [00:24:57] [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: [00:24:57] [$([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: [00:24:57] [$(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: [00:24:57] [$(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: [00:24:57] [$(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: [00:24:57] [$(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: [00:24:57] [$(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: [00:24:57] [$(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: [00:24:57] [$(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: [00:24:57] [$(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)] -147: [00:24:57] [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: [00:24:57] [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: [00:24:57] [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: [00:24:57] [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: [00:24:57] [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: [00:24:57] 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: [00:24:57] [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: [00:24:57] [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: [00:24:57] [!#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: [00:24:57] [!#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: [00:24:57] [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: [00:24:57] [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: [00:24:57] [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: [00:24:57] [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: [00:24:57] [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: [00:24:57] [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: [00:24:57] [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: [00:24:57] [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)] -147: ----------- -147: [00:24:57] [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: [00:24:57] [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: [00:24:57] [$([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: [00:24:57] [$([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: [00:24:57] [$(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: [00:24:57] [$(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: [00:24:57] [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: [00:24:57] [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: [00:24:57] 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: [00:24:57] 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: [00:24:57] [!#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: [00:24:57] [!#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: [00:24:57] [!#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: [00:24:57] [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: [00:24:57] [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: ----------- +68: [20:24:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +68: [20:24:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +126: ..[20:24:13] +126: +126: **** +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 +126: Failed Expression: atom_props.size() == num_atoms +126: ---------- +126: Stacktrace: +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# 0x00007F24ECCD243A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdMolDescriptors.so +126: 4# 0x00007F24ECCE2726 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# 0x00007F24F0CCE62C 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 +126: 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 +126: 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/rdChemReactions.so +126: 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/rdMolChemicalFeatures.so +126: 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 +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# 0x00007F24EE7B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +126: 18# 0x00007F24EE7B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +126: 19# 0x00007F24EE7B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +126: 20# 0x00007F24EE7B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +126: 21# 0x00007F24EE7B7933 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# 0x00007F24F0CCB3C6 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 +126: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 +126: 32# 0x0000000000690C6F in /usr/bin/python3 +126: 33# 0x000000000062D590 in /usr/bin/python3 +126: 34# _PyObject_MakeTpCall in /usr/bin/python3 +126: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 +126: 36# 0x00000000005CD3C9 in /usr/bin/python3 +126: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 +126: 38# 0x0000000000690C6F in /usr/bin/python3 +126: 39# 0x000000000062D590 in /usr/bin/python3 +126: 40# _PyObject_MakeTpCall in /usr/bin/python3 +126: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 +126: 42# 0x00000000005CD3C9 in /usr/bin/python3 +126: 43# _PyEval_EvalFrameDefault in /usr/bin/python3 +126: 44# 0x0000000000690C6F in /usr/bin/python3 +126: 45# 0x000000000062D590 in /usr/bin/python3 +126: 46# _PyObject_MakeTpCall in /usr/bin/python3 +126: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 +126: 48# 0x00000000005A090C in /usr/bin/python3 +126: 49# _PyObject_MakeTpCall in /usr/bin/python3 +126: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 +126: 51# PyEval_EvalCode in /usr/bin/python3 +126: 52# 0x00000000006AB8D1 in /usr/bin/python3 +126: 53# 0x00000000006A899C in /usr/bin/python3 +126: 54# 0x00000000006B9943 in /usr/bin/python3 +126: 55# 0x00000000006B93E3 in /usr/bin/python3 +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# 0x00007F24F1599CA8 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: +112/236 Test #144: testCrystalForceField .................. Passed 0.16 sec test 152 Start 152: pyMolAlign @@ -25271,82 +25487,195 @@ 152: Test timeout computed to be: 1500 68: Test 68: -68: Sotorasib_atropBad1.mrv -68: -68: [00:24:57] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 -68: Test -68: -68: Sotorasib_atropBad2.mrv +68: BMS-986142_atropBad2.mrv 68: -68: [00:24:57] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +68: [20:24:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +143: [20:24:13] done +143: [20:24:13] ------------------------------------- +143: [20:24:13] Testing UFF special cases. +143: [20:24:13] UFFTYPER: Unrecognized charge state for atom: 0 +143: [20:24:13] done +143: [20:24:13] ------------------------------------- +143: [20:24:13] Testing Issue239. +147: [20:24:13] [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: [20:24:13] [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: [20:24:13] [$([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: [20:24:13] [$([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: [20:24:13] [$(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: [20:24:13] [$(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: [20:24:13] [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: [20:24:13] [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: [20:24:13] 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: [20:24:13] 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: [20:24:13] [!#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: [20:24:13] [!#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: [20:24:13] [!#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: [20:24:13] [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: [20:24:13] [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: ----------- +69: [20:24:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +69: [20:24:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +69: [20:24:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +69: [20:24:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +147: [20:24:13] [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: [20:24:13] [$([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)] +147: [20:24:13] [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: [20:24:13] 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: ----------- +126: ...Warning: Atom Count for residue GLU5A does not match expected count +143: [20:24:13] done +143: [20:24:13] ------------------------------------- +143: [20:24:13] Testing calcEnergy with passed coords. +126: Warning: Atom Count for residue ASN39A does not match expected count +126: Warning: Atom Count for residue GLU53A does not match expected count +126: Warning: Atom Count for residue ARG64A does not match expected count +147: ----------- 127: ........ 127: ---------------------------------------------------------------------- -127: Ran 8 tests in 0.187s +127: Ran 8 tests in 0.193s 127: 127: OK -111/236 Test #115: testEEM ................................ Passed 0.70 sec -147: [00:24:57] [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: [00:24:57] [$([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)] -147: [00:24:57] [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: [00:24:57] 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: ----------- -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 -69: ---------------------------------- -69: ---------------------------------- -69: [00:24:57] +147: [20:24:13] [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: [20:24:13] [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: [20:24:13] [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: [20:24:13] [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: [20:24:13] [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: [20:24:13] [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: [20:24:13] [$(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: [20:24:13] [$(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: [20:24:13] [$(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: [20:24:13] [$(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: [20:24:13] [$(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: [20:24:13] [$(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: [20:24:13] [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: [20:24:13] [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: [20:24:13] [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: [20:24:13] [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: [20:24:13] [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: [20:24:13] [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)] +128: pass 2 +128: launch :0 +128: launch :1 +128: launch :2 +128: launch :3 +126: Warning: Atom Count for residue LYS80A does not match expected count +143: [20:24:13] done +143: [20:24:13] ------------------------------------- +143: [20:24:13] Testing calcGrad. +126: Warning: Atom Count for residue GLU150A does not match expected count +126: Warning: Atom Count for residue ASN157A does not match expected count +69: [20:24:13] deprecated group abbreviation ignored on line 24 +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: [20:24:13] 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: 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::setAtomRLabel(RDKit::Atom*, int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -69: 3# 0x0000563C49685FFF in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 4# 0x0000563C496DF3EA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 5# 0x0000563C4965F923 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 6# 0x00007F4415233CA8 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# 0x0000563C4965FAD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +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# 0x00007FED9A6C8531 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 4# 0x00007FED9A6D1DFA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 5# 0x00007FED9A6D217D 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# 0x000055CD737E6C15 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 10# 0x000055CD7384D372 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 11# 0x000055CD737CD923 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 12# 0x00007FED99C33CA8 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# 0x000055CD737CDAD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 69: ---------- 69: **** 69: -69: [00:24:57] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -147: ----------- -147: [00:24:57] [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: [00:24:57] [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: [00:24:57] [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: [00:24:57] [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: [00:24:57] [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: [00:24:57] [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)] -112/236 Test #144: testCrystalForceField .................. Passed 0.15 sec -147: [00:24:57] [$(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: [00:24:57] [$(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: [00:24:57] [$(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: [00:24:57] [$(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: [00:24:57] [$(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: [00:24:57] [$(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)] -test 154 - Start 154: pyChemicalFeatures +143: [20:24:13] done +143: [20:24:13] ------------------------------------- +143: [20:24:13] Testing SFIssue1653802. +143: [20:24:13] done +143: [20:24:13] ------------------------------------- +143: [20:24:13] Testing SFIssue2378119. +143: [20:24:13] done +143: [20:24:13] ------------------------------------- +143: [20:24:13] Test UFF force-field parameter getters. +143: [20:24:13] ------------------------------------- +143: [20:24:13] Testing handling missing parameters. +143: [20:24:13] UFFTYPER: Unrecognized hybridization for atom: 0 +143: [20:24:13] UFFTYPER: Unrecognized atom type: Cu+1 (0) +113/236 Test #134: pyTestMHFP ............................. Passed 0.37 sec +test 153 + Start 153: testFeatures -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 -147: [00:24:57] [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: [00:24:57] [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: [00:24:57] [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: [00:24:57] [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: [00:24:57] [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: [00:24:57] [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)] -109: [00:24:57] +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 +139: ........ +139: ---------------------------------------------------------------------- +139: Ran 8 tests in 0.032s +139: +139: OK +143: [20:24:13] UFFTYPER: Unrecognized hybridization for atom: 0 +143: [20:24:13] UFFTYPER: Unrecognized atom type: Cu+1 (0) +143: [20:24:13] done +143: [20:24:13] ------------------------------------- +143: [20:24:13] Testing SFIssue3009337. +143: [20:24:13] done +143: [20:24:13] ------------------------------------- +143: [20:24:13] Test UFF multithreading +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: [20:24:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +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: [20:24:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +68: [20:24:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +68: Test +68: +68: RP-6306_atropBad1.mrv +68: +68: [20:24:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +125: Warning: Atom Count for residue GLU53A does not match expected count +109: [20:24:13] 109: 109: **** 109: Invariant Violation @@ -25357,17 +25686,17 @@ 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# 0x00007FC492C30DFD in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 +109: 2# 0x00007F691844DDFD 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# 0x0000558DF91E71FC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 5# 0x0000558DF91E46A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 6# 0x00007FC491E33CA8 in /lib/x86_64-linux-gnu/libc.so.6 +109: 4# 0x00005581EF9371FC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 5# 0x00005581EF9346A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 6# 0x00007F6917833CA8 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# 0x0000558DF91E47D1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 8# 0x00005581EF9347D1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 109: ---------- 109: **** 109: -109: [00:24:57] +109: [20:24:13] 109: 109: **** 109: Invariant Violation @@ -25378,17 +25707,17 @@ 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# 0x00007FC492C30DFD in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 +109: 2# 0x00007F691844DDFD 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# 0x0000558DF91E71FC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 5# 0x0000558DF91E46A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 6# 0x00007FC491E33CA8 in /lib/x86_64-linux-gnu/libc.so.6 +109: 4# 0x00005581EF9371FC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 5# 0x00005581EF9346A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 6# 0x00007F6917833CA8 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# 0x0000558DF91E47D1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 8# 0x00005581EF9347D1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 109: ---------- 109: **** 109: -109: [00:24:57] +109: [20:24:13] 109: 109: **** 109: Invariant Violation @@ -25399,192 +25728,138 @@ 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# 0x00007FC492C30DFD in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 +109: 2# 0x00007F691844DDFD 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# 0x0000558DF91E71FC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 5# 0x0000558DF91E46A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 6# 0x00007FC491E33CA8 in /lib/x86_64-linux-gnu/libc.so.6 +109: 4# 0x00005581EF9371FC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 5# 0x00005581EF9346A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 6# 0x00007F6917833CA8 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# 0x0000558DF91E47D1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 8# 0x00005581EF9347D1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 109: ---------- 109: **** 109: -113/236 Test #109: testFragCatalog ........................ Passed 0.87 sec -153: [00:24:57] ------------------------------------- -153: [00:24:57] AtomType parser testing. -153: [00:24:57] SMARTS Parse Error: syntax error while parsing: [$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103] -153: [00:24:57] 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: [00:24:57] done -153: [00:24:57] ------------------------------------- -153: [00:24:57] FeatureDefinition parser testing. -153: [00:24:57] done -153: [00:24:57] ------------------------------------- -153: [00:24:57] Test pulling feat defs from a string. -153: [00:24:57] done -153: [00:24:57] ------------------------------------- -153: [00:24:57] FeatureDef functionality testing. +133: .............. +133: ---------------------------------------------------------------------- +133: Ran 14 tests in 0.164s +133: +133: OK +114/236 Test #109: testFragCatalog ........................ Passed 0.85 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 +143: generating reference data +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: *********************************************************** +130: [20:24:13] done +130: [20:24:13] ------------------------------------- +130: [20:24:13] Test unfolded version of RDKFP +130: [20:24:13] ------------------------------------- +130: [20:24:13] Test topological torsion fp generator +130: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +68: Test +68: +68: RP-6306_atropBad2.mrv +68: +68: [20:24:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +68: [20:24:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +68: [20:24:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +153: [20:24:13] ------------------------------------- +153: [20:24:13] AtomType parser testing. +153: [20:24:13] SMARTS Parse Error: syntax error while parsing: [$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103] +153: [20:24:13] 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: [20:24:13] done +153: [20:24:13] ------------------------------------- +153: [20:24:13] FeatureDefinition parser testing. +151: Randomness seeded to: 2490148208 +151: 57262214 +115/236 Test #127: pyMolDescriptors3D ..................... Passed 0.58 sec +116/236 Test #149: testMolAlign ........................... Passed 0.16 sec +153: [20:24:13] done +153: [20:24:13] ------------------------------------- +153: [20:24:13] Test pulling feat defs from a string. +153: [20:24:13] done +153: [20:24:13] ------------------------------------- +153: [20:24:13] FeatureDef functionality testing. +126: Warning: Atom Count for residue GLU5A does not match expected count 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 -125: Warning: Atom Count for residue ASN39A does not match expected count -126: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -126: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -126: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -126: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -126: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -126: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -126: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -126: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -126: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -126: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -126: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -126: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -126: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [00:24:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: ..[00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -126: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -126: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -126: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -126: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -126: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -126: .[00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -126: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -126: [00:24:57] DEPRECATION WARNING: please use AtomPairGenerator -114/236 Test #127: pyMolDescriptors3D ..................... Passed 0.53 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 -151: Randomness seeded to: 3291328841 -151: 67403487 -126: ..[00:24:57] -126: -126: **** -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 -126: Failed Expression: atom_props.size() == num_atoms -126: ---------- -126: Stacktrace: -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# 0x00007F11DC2AA43A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdMolDescriptors.so -126: 4# 0x00007F11DC2BA726 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# 0x00007F11E02B162C 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 -126: 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 -126: 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/rdChemReactions.so -126: 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/rdMolChemicalFeatures.so -126: 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 -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# 0x00007F11DDDB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -126: 18# 0x00007F11DDDB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -126: 19# 0x00007F11DDDB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -126: 20# 0x00007F11DDDB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -126: 21# 0x00007F11DDDB7933 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# 0x00007F11E02AE3C6 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 -126: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 -126: 32# 0x0000000000690C6F in /usr/bin/python3 -126: 33# 0x000000000062D590 in /usr/bin/python3 -126: 34# _PyObject_MakeTpCall in /usr/bin/python3 -126: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 -126: 36# 0x00000000005CD3C9 in /usr/bin/python3 -126: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 -126: 38# 0x0000000000690C6F in /usr/bin/python3 -126: 39# 0x000000000062D590 in /usr/bin/python3 -126: 40# _PyObject_MakeTpCall in /usr/bin/python3 -126: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 -126: 42# 0x00000000005CD3C9 in /usr/bin/python3 -126: 43# _PyEval_EvalFrameDefault in /usr/bin/python3 -126: 44# 0x0000000000690C6F in /usr/bin/python3 -126: 45# 0x000000000062D590 in /usr/bin/python3 -126: 46# _PyObject_MakeTpCall in /usr/bin/python3 -126: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 -126: 48# 0x00000000005A090C in /usr/bin/python3 -126: 49# _PyObject_MakeTpCall in /usr/bin/python3 -126: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 -126: 51# PyEval_EvalCode in /usr/bin/python3 -126: 52# 0x00000000006AB8D1 in /usr/bin/python3 -126: 53# 0x00000000006A899C in /usr/bin/python3 -126: 54# 0x00000000006B9943 in /usr/bin/python3 -126: 55# 0x00000000006B93E3 in /usr/bin/python3 -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# 0x00007F11E0B7CCA8 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: -153: [00:24:57] done -153: [00:24:57] ------------------------------------- -153: [00:24:57] FeatureFactory testing. -153: [00:24:57] 1 -153: [00:24:57] 2 -153: [00:24:57] 3 -153: [00:24:57] 4 -153: [00:24:57] 5 -153: [00:24:57] 6 -153: [00:24:57] done -153: [00:24:57] ------------------------------------- -153: [00:24:57] Feature Location testing. -153: [00:24:57] done -153: [00:24:57] ------------------------------------- -153: [00:24:57] Test building a FeatureFactory from a file -153: [00:24:57] done -153: [00:24:57] ------------------------------------- -153: [00:24:57] Testing Issue 224. -153: [00:24:57] done -153: [00:24:57] ------------------------------------- -153: [00:24:57] Testing Issue 225. -153: [00:24:57] done -153: [00:24:57] ------------------------------------- -153: [00:24:57] Test Issue346 -153: [00:24:57] done -153: [00:24:57] ------------------------------------- -153: [00:24:57] Test Issue347 -153: [00:24:57] done -153: [00:24:57] ------------------------------------- -153: [00:24:57] Testing Issue 348. -153: [00:24:57] SMARTS Parse Error: syntax error while parsing: [C[C] -153: [00:24:57] SMARTS Parse Error: Failed parsing SMARTS '[C[C]' for input: '[C[C]' -153: [00:24:57] ------------------------------------- -153: [00:24:57] Testing Nested AtomType definitions. +153: [20:24:13] done +153: [20:24:13] ------------------------------------- +153: [20:24:13] FeatureFactory testing. +153: [20:24:13] 1 +153: [20:24:13] 2 +153: [20:24:13] 3 +153: [20:24:13] 4 +153: [20:24:13] 5 +153: [20:24:13] 6 +153: [20:24:13] done +153: [20:24:13] ------------------------------------- +153: [20:24:13] Feature Location testing. +153: [20:24:13] done +153: [20:24:13] ------------------------------------- +153: [20:24:13] Test building a FeatureFactory from a file +153: [20:24:13] done +153: [20:24:13] ------------------------------------- +153: [20:24:13] Testing Issue 224. +153: [20:24:13] done +153: [20:24:13] ------------------------------------- +153: [20:24:13] Testing Issue 225. +153: [20:24:13] done +153: [20:24:13] ------------------------------------- +153: [20:24:13] Test Issue346 +153: [20:24:13] done +153: [20:24:13] ------------------------------------- +153: [20:24:13] Test Issue347 +153: [20:24:13] done +153: [20:24:13] ------------------------------------- +153: [20:24:13] Testing Issue 348. +153: [20:24:13] SMARTS Parse Error: syntax error while parsing: [C[C] +153: [20:24:13] SMARTS Parse Error: Failed parsing SMARTS '[C[C]' for input: '[C[C]' +153: [20:24:13] ------------------------------------- +153: [20:24:13] Testing Nested AtomType definitions. 153: [$([$([$([C;!$(C=[O,N,P,S]);!$(C#N)]),c]);R])] -153: [00:24:57] ------------------------------------- -153: [00:24:57] Testing Github Issue #252: crash when calling getPos() with no conformer. -153: [00:24:57] expect a precondition failure message below -153: [00:24:57] +153: [20:24:13] ------------------------------------- +153: [20:24:13] Testing Github Issue #252: crash when calling getPos() with no conformer. +153: [20:24:13] expect a precondition failure message below +153: [20:24:13] 153: 153: **** 153: Pre-condition Violation @@ -25597,191 +25872,142 @@ 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# 0x000056361682FE50 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures -153: 5# 0x0000563616824743 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures -153: 6# 0x00007F8F98233CA8 in /lib/x86_64-linux-gnu/libc.so.6 +153: 4# 0x0000562ACA551E50 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures +153: 5# 0x0000562ACA546743 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures +153: 6# 0x00007FC4E9233CA8 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# 0x0000563616824841 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures +153: 8# 0x0000562ACA546841 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures 153: ---------- 153: **** 153: -153: [00:24:57] Done -153: [00:24:57] ------------------------------------- -153: [00:24:57] Testing github 2077: add confId argument to MolChemicalFeatureFactor::getFeaturesForMol() -153: [00:24:57] done -115/236 Test #153: testFeatures ........................... Passed 0.05 sec +153: [20:24:13] Done +153: [20:24:13] ------------------------------------- +153: [20:24:13] Testing github 2077: add confId argument to MolChemicalFeatureFactor::getFeaturesForMol() +153: [20:24:13] done +130: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [20:24:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [20:24:13] done +130: [20:24:13] ------------------------------------- +130: [20:24:13] Test Topological Torsions. +130: [20:24:13] done +130: [20:24:13] ------------------------------------- +130: [20:24:13] Test Folded torsions. +147: [20:24:13] UFFTYPER: Unrecognized atom type: Pt5+2 (1) +117/236 Test #139: pyMolTransforms ........................ Passed 0.38 sec +118/236 Test #153: testFeatures ........................... Passed 0.09 sec test 157 Start 157: testMolCatalog 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 -141: [00:24:57] done -141: [00:24:57] ------------------------------------- -141: [00:24:57] Testing github 308: crash during MMFF parameterization . -141: [00:24:57] ------------------------------------- -141: [00:24:57] Testing SFIssue1653802. -141: [00:24:57] done -141: [00:24:57] ------------------------------------- -141: [00:24:57] Testing SFIssue2378119. -141: [00:24:57] done -141: [00:24:57] ------------------------------------- -141: [00:24:57] Test MMFF force-field parameter getters. -141: [00:24:57] ------------------------------------- -141: [00:24:57] Test MMFF multithreading -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: [00:24:57] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -126: ...Warning: Atom Count for residue GLU5A does not match expected count -119: =>start test MORSE -119: =>read file -119: [00:24:57] test on : 365 molecules done -116/236 Test #119: testMORSE .............................. Passed 0.76 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 -126: Warning: Atom Count for residue ASN39A does not match expected count -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 -141: generating reference data -139: ........ -139: ---------------------------------------------------------------------- -139: Ran 8 tests in 0.036s -139: -139: OK -147: [00:24:57] UFFTYPER: Unrecognized atom type: Pt5+2 (1) -155: *********************************************************** -155: Testing ShapeHelpers -155: --------------------------------- -155: test1Encode -155: -155: --------------------------------- -155: test2Compare -155: -155: --------------------------------- -155: testGithub4364 -155: -155: *********************************************************** -126: Warning: Atom Count for residue GLU150A does not match expected count -117/236 Test #155: testShapeHelpers ....................... Passed 0.06 sec -126: Warning: Atom Count for residue ASN157A does not match expected count -147: [00:24:57] UFFTYPER: Unrecognized charge state for atom: 1 -147: [00:24:57] UFFTYPER: Unrecognized charge state for atom: 1 -147: [00:24:57] UFFTYPER: Unrecognized charge state for atom: 1 -120: [00:24:57] done -120: [00:24:57] ------------------------------------- -120: [00:24:57] PMI edge cases. -120: [00:24:57] done -120: [00:24:57] ------------------------------------- -120: [00:24:57] NPR edge cases. -120: [00:24:57] done -120: [00:24:57] ------------------------------------- -120: [00:24:57] 3D descriptors. -120: [00:24:57] done -120: [00:24:57] ------------------------------------- -120: [00:24:57] 3D descriptor edge cases. -120: [00:24:57] done -120: [00:24:57] ------------------------------------- -120: [00:24:57] Inertial shape factor. -120: [00:24:57] done -151: 58747357 +125: Warning: Atom Count for residue ARG64A does not match expected count +130: [20:24:13] done +130: [20:24:13] ------------------------------------- +130: [20:24:13] Test Bulk Topological Torsions. +145: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [20:24:13] Molecule does not have explicit Hs. Consider calling AddHs() +145: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [20:24:13] Molecule does not have explicit Hs. Consider calling AddHs() +145: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [20:24:13] Molecule does not have explicit Hs. Consider calling AddHs() +145: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [20:24:13] Molecule does not have explicit Hs. Consider calling AddHs() +145: [20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [20:24:13] Molecule does not have explicit Hs. Consider calling AddHs() +145: ..[20:24:13] Molecule does not have explicit Hs. Consider calling AddHs() +145: [20:24:13] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [20:24:13] Molecule does not have explicit Hs. Consider calling AddHs() +147: [20:24:13] UFFTYPER: Unrecognized charge state for atom: 1 68: Test 68: -68: mrtx1719_3d.mrv +68: RP-6306_3d.mrv 68: 68: Test 68: -68: mrtx1719_atrop1.mrv +68: Sotorasib_atrop1.mrv 68: 68: Test 68: -68: mrtx1719_atrop2.mrv +68: Sotorasib_atrop2.mrv 68: 68: Test 68: -68: mrtx1719_atrop3.mrv +68: Sotorasib_atrop3.mrv 68: 68: Test 68: -68: mrtx1719_atropBad1.mrv +68: Sotorasib_atrop4.mrv 68: -68: [00:24:57] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -130: [00:24:57] done -130: [00:24:57] ------------------------------------- -130: [00:24:57] Test Rooted Topological Torsions. -130: [00:24:57] done -130: [00:24:57] ------------------------------------- -130: [00:24:57] Test ignoring atoms in Topological Torsions. -130: [00:24:57] done -130: [00:24:57] ------------------------------------- -130: [00:24:57] ------------------------------------- -130: [00:24:57] Test Topological Torsions including info about chirality. -130: [00:24:57] done -130: [00:24:57] ------------------------------------- -130: [00:24:57] Test GitHub Issue 25: fingerprint backwards compatibility. -130: [00:24:57] done -130: [00:24:57] ------------------------------------- -130: [00:24:57] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. -130: [00:24:57] done -130: [00:24:57] ------------------------------------- -130: [00:24:57] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 -130: [00:24:57] done -130: [00:24:57] ------------------------------------- -130: [00:24:57] Test convenience and bulk fp calculation functions -136: ....... -136: ---------------------------------------------------------------------- -136: Ran 7 tests in 0.169s -136: -136: OK -142: done -142: [00:24:57] done -143: [00:24:57] done -143: [00:24:57] ------------------------------------- -143: [00:24:57] Testing UFF special cases. -143: [00:24:57] UFFTYPER: Unrecognized charge state for atom: 0 -143: [00:24:57] done -143: [00:24:57] ------------------------------------- -143: [00:24:57] Testing Issue239. +68: Test +68: +68: Sotorasib_atrop5.mrv +68: +68: [20:24:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +68: [20:24:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +151: 56200237 +89: [20:24:13] Explicit valence for atom # 2 O, 4, is greater than permitted +119/236 Test #133: pyTestGenerator ........................ Passed 0.51 sec +120/236 Test #157: testMolCatalog ......................... Passed 0.02 sec 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 -118/236 Test #120: test3D ................................. Passed 0.83 sec -119/236 Test #139: pyMolTransforms ........................ Passed 0.39 sec -120/236 Test #157: testMolCatalog ......................... Passed 0.11 sec -143: [00:24:57] done -143: [00:24:57] ------------------------------------- -143: [00:24:57] Testing calcEnergy with passed coords. +136: ....... +136: ---------------------------------------------------------------------- +136: Ran 7 tests in 0.166s +136: +136: OK 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 +147: [20:24:13] UFFTYPER: Unrecognized charge state for atom: 1 +147: [20:24:13] UFFTYPER: Unrecognized charge state for atom: 1 +145: .[20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [20:24:13] Molecule does not have explicit Hs. Consider calling AddHs() +68: Test +68: +68: Sotorasib_atropBad1.mrv +68: +68: [20:24:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +68: Test +68: +68: Sotorasib_atropBad2.mrv +68: +68: [20:24:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +89: [20:24:13] Explicit valence for atom # 3 Al, 6, is greater than permitted +89: [20:24:13] Explicit valence for atom # 3 Be, 4, is greater than permitted +89: [20:24:13] Explicit valence for atom # 27 P, 6, is greater than permitted +119: =>start test MORSE +119: =>read file +119: [20:24:13] test on : 365 molecules done +155: *********************************************************** +155: Testing ShapeHelpers +155: --------------------------------- +155: test1Encode +155: +155: --------------------------------- +155: test2Compare +155: +155: --------------------------------- +155: testGithub4364 +155: +155: *********************************************************** +121/236 Test #119: testMORSE .............................. Passed 0.85 sec +122/236 Test #155: testShapeHelpers ....................... Passed 0.08 sec test 161 Start 161: moldraw2DRxnTest1 @@ -25794,424 +26020,440 @@ 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 -89: [00:24:57] Explicit valence for atom # 9 N, 5, is greater than permitted -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: *********************************************************** -121/236 Test #149: testMolAlign ........................... Passed 0.29 sec -125: Warning: Atom Count for residue GLU53A does not match expected count -143: [00:24:57] done -143: [00:24:57] ------------------------------------- -143: [00:24:57] Testing calcGrad. -143: [00:24:57] done -143: [00:24:57] ------------------------------------- -143: [00:24:57] Testing SFIssue1653802. -143: [00:24:57] done -143: [00:24:57] ------------------------------------- -143: [00:24:57] Testing SFIssue2378119. -143: [00:24:57] done -143: [00:24:57] ------------------------------------- -143: [00:24:57] Test UFF force-field parameter getters. -143: [00:24:57] ------------------------------------- -143: [00:24:57] Testing handling missing parameters. -143: [00:24:57] UFFTYPER: Unrecognized hybridization for atom: 0 -143: [00:24:57] UFFTYPER: Unrecognized atom type: Cu+1 (0) -143: [00:24:57] UFFTYPER: Unrecognized hybridization for atom: 0 -143: [00:24:57] UFFTYPER: Unrecognized atom type: Cu+1 (0) -143: [00:24:57] done -143: [00:24:57] ------------------------------------- -143: [00:24:57] Testing SFIssue3009337. -143: [00:24:57] done -143: [00:24:57] ------------------------------------- -143: [00:24:57] Test UFF multithreading +145: .[20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [20:24:13] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[20:24:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [20:24:13] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[20:24:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[20:24:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[20:24:14] UFFTYPER: Unrecognized hybridization for atom: 0 +145: [20:24:14] UFFTYPER: Unrecognized atom type: Cu+1 (0) +145: .[20:24:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +145: [20:24:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +145: [20:24:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +159: ----------------- Test 1 +123/236 Test #136: pyPartialCharges ....................... Passed 0.52 sec +145: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() 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 -126: Warning: Atom Count for residue GLU5A does not match expected count -122/236 Test #142: testMMFFForceFieldHelpersMultiThread ... Passed 0.43 sec -133: .............. -133: ---------------------------------------------------------------------- -133: Ran 14 tests in 0.211s -133: -133: OK -123/236 Test #136: pyPartialCharges ....................... Passed 0.55 sec -108: .............[00:24:57] SMILES Parse Error: syntax error while parsing: --- -108: [00:24:57] SMILES Parse Error: check for mistakes around position 1: -108: [00:24:57] --- -108: [00:24:57] ^ -108: [00:24:57] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [00:24:57] dasfsadf -108: [00:24:57] SMILES Parse Error: syntax error while parsing: --- -108: [00:24:57] SMILES Parse Error: check for mistakes around position 1: -108: [00:24:57] --- -108: [00:24:57] ^ -108: [00:24:57] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [00:24:57] dasfsadf -108: [00:24:57] SMILES Parse Error: syntax error while parsing: --- -108: [00:24:57] SMILES Parse Error: check for mistakes around position 1: -108: [00:24:57] --- -108: [00:24:57] ^ -108: [00:24:57] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [00:24:57] dasfsadf -108: [00:24:57] SMILES Parse Error: syntax error while parsing: --- -108: [00:24:57] SMILES Parse Error: check for mistakes around position 1: -108: [00:24:57] --- -108: [00:24:57] ^ -108: [00:24:57] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [00:24:57] dasfsadf -108: [00:24:57] SMILES Parse Error: syntax error while parsing: --- -108: [00:24:57] SMILES Parse Error: check for mistakes around position 1: -108: [00:24:57] --- -108: [00:24:57] ^ -108: [00:24:57] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [00:24:57] dasfsadf -108: [00:24:57] SMILES Parse Error: syntax error while parsing: --- -108: [00:24:57] SMILES Parse Error: check for mistakes around position 1: -108: [00:24:57] --- -108: [00:24:57] ^ -108: [00:24:57] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [00:24:57] dasfsadf -108: [00:24:57] SMILES Parse Error: syntax error while parsing: --- -108: [00:24:57] SMILES Parse Error: check for mistakes around position 1: -108: [00:24:57] --- -108: [00:24:57] ^ -108: [00:24:57] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [00:24:57] dasfsadf -108: [00:24:57] SMILES Parse Error: syntax error while parsing: --- -108: [00:24:57] SMILES Parse Error: check for mistakes around position 1: -108: [00:24:57] --- -108: [00:24:57] ^ -108: [00:24:57] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [00:24:57] dasfsadf -108: [00:24:57] SMILES Parse Error: syntax error while parsing: --- -108: [00:24:57] SMILES Parse Error: check for mistakes around position 1: -108: [00:24:57] --- -108: [00:24:57] ^ -108: [00:24:57] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [00:24:57] dasfsadf -108: [00:24:57] SMILES Parse Error: syntax error while parsing: --- -108: [00:24:57] SMILES Parse Error: check for mistakes around position 1: -108: [00:24:57] --- -108: [00:24:57] ^ -108: [00:24:57] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [00:24:57] dasfsadf -108: [00:24:57] SMILES Parse Error: syntax error while parsing: --- -108: [00:24:57] SMILES Parse Error: check for mistakes around position 1: -108: [00:24:57] --- -108: [00:24:57] ^ -108: [00:24:57] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [00:24:57] dasfsadf -108: [00:24:57] SMILES Parse Error: syntax error while parsing: --- -108: [00:24:57] SMILES Parse Error: check for mistakes around position 1: -108: [00:24:57] --- -108: [00:24:57] ^ -108: [00:24:57] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [00:24:57] dasfsadf -108: [00:24:57] SMILES Parse Error: syntax error while parsing: --- -108: [00:24:57] SMILES Parse Error: check for mistakes around position 1: -108: [00:24:57] --- -108: [00:24:57] ^ -108: [00:24:57] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [00:24:57] dasfsadf -108: [00:24:57] SMILES Parse Error: syntax error while parsing: --- -108: [00:24:57] SMILES Parse Error: check for mistakes around position 1: -108: [00:24:57] --- -108: [00:24:57] ^ -108: [00:24:57] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [00:24:57] dasfsadf -108: [00:24:57] SMILES Parse Error: syntax error while parsing: --- -108: [00:24:57] SMILES Parse Error: check for mistakes around position 1: -108: [00:24:57] --- -108: [00:24:57] ^ -108: [00:24:57] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [00:24:57] dasfsadf -108: [00:24:57] SMILES Parse Error: syntax error while parsing: --- -108: [00:24:57] SMILES Parse Error: check for mistakes around position 1: -108: [00:24:57] --- -108: [00:24:57] ^ -108: [00:24:57] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [00:24:57] dasfsadf -108: [00:24:57] SMILES Parse Error: syntax error while parsing: --- -108: [00:24:57] SMILES Parse Error: check for mistakes around position 1: -108: [00:24:57] --- -108: [00:24:57] ^ -108: [00:24:57] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [00:24:57] dasfsadf -108: [00:24:57] SMILES Parse Error: syntax error while parsing: --- -108: [00:24:57] SMILES Parse Error: check for mistakes around position 1: -108: [00:24:57] --- -108: [00:24:57] ^ -108: [00:24:57] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [00:24:57] dasfsadf -108: [00:24:57] SMILES Parse Error: syntax error while parsing: --- -108: [00:24:57] SMILES Parse Error: check for mistakes around position 1: -108: [00:24:57] --- -108: [00:24:57] ^ -108: [00:24:57] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [00:24:57] dasfsadf -108: [00:24:57] SMILES Parse Error: syntax error while parsing: --- -108: [00:24:57] SMILES Parse Error: check for mistakes around position 1: -108: [00:24:57] --- -108: [00:24:57] ^ -108: [00:24:57] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [00:24:57] dasfsadf -108: [00:24:57] SMILES Parse Error: syntax error while parsing: --- -108: [00:24:57] SMILES Parse Error: check for mistakes around position 1: -108: [00:24:57] --- -108: [00:24:57] ^ -108: [00:24:57] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [00:24:57] dasfsadf -108: [00:24:57] SMILES Parse Error: syntax error while parsing: --- -108: [00:24:57] SMILES Parse Error: check for mistakes around position 1: -108: [00:24:57] --- -108: [00:24:57] ^ -108: [00:24:57] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [00:24:57] dasfsadf -108: [00:24:57] SMILES Parse Error: syntax error while parsing: --- -108: [00:24:57] SMILES Parse Error: check for mistakes around position 1: -108: [00:24:57] --- -108: [00:24:57] ^ -108: [00:24:57] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [00:24:57] dasfsadf -108: [00:24:57] SMILES Parse Error: syntax error while parsing: --- -108: [00:24:57] SMILES Parse Error: check for mistakes around position 1: -108: [00:24:57] --- -108: [00:24:57] ^ -108: [00:24:57] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [00:24:57] dasfsadf -108: [00:24:57] SMILES Parse Error: syntax error while parsing: --- -108: [00:24:57] SMILES Parse Error: check for mistakes around position 1: -108: [00:24:57] --- -108: [00:24:57] ^ -108: [00:24:57] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [00:24:57] dasfsadf -108: [00:24:57] SMILES Parse Error: syntax error while parsing: --- -108: [00:24:57] SMILES Parse Error: check for mistakes around position 1: -108: [00:24:57] --- -108: [00:24:57] ^ -108: [00:24:57] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [00:24:57] dasfsadf -108: [00:24:57] SMILES Parse Error: syntax error while parsing: --- -108: [00:24:57] SMILES Parse Error: check for mistakes around position 1: -108: [00:24:57] --- -108: [00:24:57] ^ -108: [00:24:57] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [00:24:57] dasfsadf -108: [00:24:57] SMILES Parse Error: syntax error while parsing: --- -108: [00:24:57] SMILES Parse Error: check for mistakes around position 1: -108: [00:24:57] --- -108: [00:24:57] ^ -108: [00:24:57] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [00:24:57] dasfsadf -108: [00:24:57] SMILES Parse Error: syntax error while parsing: --- -108: [00:24:57] SMILES Parse Error: check for mistakes around position 1: -108: [00:24:57] --- -108: [00:24:57] ^ -108: [00:24:57] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [00:24:57] dasfsadf -108: [00:24:57] SMILES Parse Error: syntax error while parsing: --- -108: [00:24:57] SMILES Parse Error: check for mistakes around position 1: -108: [00:24:57] --- -108: [00:24:57] ^ -108: [00:24:57] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [00:24:57] dasfsadf -147: [00:24:57] UFFTYPER: Unrecognized charge state for atom: 5 -147: [00:24:57] UFFTYPER: Unrecognized charge state for atom: 5 -147: [00:24:57] UFFTYPER: Unrecognized charge state for atom: 5 -159: ----------------- Test 1 -161: ----------------- Test 1 -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 -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 -160: Randomness seeded to: 2038159195 -160: file testAtomTags_3.svg gave hash 1931256064U not the expected 2244078420U -125: Warning: Atom Count for residue ARG64A does not match expected count +145: [20:24:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +145: [20:24:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[20:24:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[20:24:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +145: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +145: ...[20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +145: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() 159: file test1_5.svg gave hash 2383324771U not the expected 2811480876U -159: Done -159: ----------------- Test 2 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: Sotorasib_3d.mrv 68: 68: Test 68: -68: BMS-986142_atrop1.mrv +68: ZM374979_atrop1.mrv 68: 68: Test 68: -68: BMS-986142_atrop2.mrv +68: ZM374979_atrop2.mrv 68: 68: Test 68: -68: BMS-986142_atrop3.mrv +68: ZM374979_atrop3.mrv 68: 68: Test 68: -68: BMS-986142_atrop4.mrv +68: ZM374979_atropBad1.mrv 68: +68: [20:24:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +159: Done +159: ----------------- Test 2 +161: ----------------- Test 1 +108: .............[20:24:14] SMILES Parse Error: syntax error while parsing: --- +108: [20:24:14] SMILES Parse Error: check for mistakes around position 1: +108: [20:24:14] --- +108: [20:24:14] ^ +108: [20:24:14] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [20:24:14] dasfsadf +108: [20:24:14] SMILES Parse Error: syntax error while parsing: --- +108: [20:24:14] SMILES Parse Error: check for mistakes around position 1: +108: [20:24:14] --- +108: [20:24:14] ^ +108: [20:24:14] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [20:24:14] dasfsadf +108: [20:24:14] SMILES Parse Error: syntax error while parsing: --- +108: [20:24:14] SMILES Parse Error: check for mistakes around position 1: +108: [20:24:14] --- +108: [20:24:14] ^ +108: [20:24:14] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [20:24:14] dasfsadf +108: [20:24:14] SMILES Parse Error: syntax error while parsing: --- +108: [20:24:14] SMILES Parse Error: check for mistakes around position 1: +108: [20:24:14] --- +108: [20:24:14] ^ +108: [20:24:14] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [20:24:14] dasfsadf +108: [20:24:14] SMILES Parse Error: syntax error while parsing: --- +108: [20:24:14] SMILES Parse Error: check for mistakes around position 1: +108: [20:24:14] --- +108: [20:24:14] ^ +108: [20:24:14] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [20:24:14] dasfsadf +108: [20:24:14] SMILES Parse Error: syntax error while parsing: --- +108: [20:24:14] SMILES Parse Error: check for mistakes around position 1: +108: [20:24:14] --- +108: [20:24:14] ^ +108: [20:24:14] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [20:24:14] dasfsadf +108: [20:24:14] SMILES Parse Error: syntax error while parsing: --- +108: [20:24:14] SMILES Parse Error: check for mistakes around position 1: +108: [20:24:14] --- +108: [20:24:14] ^ +108: [20:24:14] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [20:24:14] dasfsadf +108: [20:24:14] SMILES Parse Error: syntax error while parsing: --- +108: [20:24:14] SMILES Parse Error: check for mistakes around position 1: +108: [20:24:14] --- +108: [20:24:14] ^ +108: [20:24:14] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [20:24:14] dasfsadf +147: [20:24:14] UFFTYPER: Unrecognized charge state for atom: 5 +145: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +108: [20:24:14] SMILES Parse Error: syntax error while parsing: --- +108: [20:24:14] SMILES Parse Error: check for mistakes around position 1: +108: [20:24:14] --- +108: [20:24:14] ^ +108: [20:24:14] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [20:24:14] dasfsadf +108: [20:24:14] SMILES Parse Error: syntax error while parsing: --- +108: [20:24:14] SMILES Parse Error: check for mistakes around position 1: +108: [20:24:14] --- +108: [20:24:14] ^ +108: [20:24:14] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [20:24:14] dasfsadf +147: [20:24:14] UFFTYPER: Unrecognized charge state for atom: 5 +108: [20:24:14] SMILES Parse Error: syntax error while parsing: --- +108: [20:24:14] SMILES Parse Error: check for mistakes around position 1: +108: [20:24:14] --- +108: [20:24:14] ^ +108: [20:24:14] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [20:24:14] dasfsadf +108: [20:24:14] SMILES Parse Error: syntax error while parsing: --- +108: [20:24:14] SMILES Parse Error: check for mistakes around position 1: +108: [20:24:14] --- +108: [20:24:14] ^ +108: [20:24:14] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [20:24:14] dasfsadf +108: [20:24:14] SMILES Parse Error: syntax error while parsing: --- +108: [20:24:14] SMILES Parse Error: check for mistakes around position 1: +108: [20:24:14] --- +108: [20:24:14] ^ +108: [20:24:14] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [20:24:14] dasfsadf +108: [20:24:14] SMILES Parse Error: syntax error while parsing: --- +108: [20:24:14] SMILES Parse Error: check for mistakes around position 1: +108: [20:24:14] --- +108: [20:24:14] ^ +108: [20:24:14] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [20:24:14] dasfsadf +108: [20:24:14] SMILES Parse Error: syntax error while parsing: --- +108: [20:24:14] SMILES Parse Error: check for mistakes around position 1: +108: [20:24:14] --- +108: [20:24:14] ^ +108: [20:24:14] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [20:24:14] dasfsadf +108: [20:24:14] SMILES Parse Error: syntax error while parsing: --- +108: [20:24:14] SMILES Parse Error: check for mistakes around position 1: +108: [20:24:14] --- +108: [20:24:14] ^ +108: [20:24:14] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [20:24:14] dasfsadf +108: [20:24:14] SMILES Parse Error: syntax error while parsing: --- +108: [20:24:14] SMILES Parse Error: check for mistakes around position 1: +108: [20:24:14] --- +108: [20:24:14] ^ +108: [20:24:14] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [20:24:14] dasfsadf +108: [20:24:14] SMILES Parse Error: syntax error while parsing: --- +108: [20:24:14] SMILES Parse Error: check for mistakes around position 1: +108: [20:24:14] --- +108: [20:24:14] ^ +108: [20:24:14] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [20:24:14] dasfsadf +108: [20:24:14] SMILES Parse Error: syntax error while parsing: --- +108: [20:24:14] SMILES Parse Error: check for mistakes around position 1: +108: [20:24:14] --- +108: [20:24:14] ^ +108: [20:24:14] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [20:24:14] dasfsadf +108: [20:24:14] SMILES Parse Error: syntax error while parsing: --- +108: [20:24:14] SMILES Parse Error: check for mistakes around position 1: +108: [20:24:14] --- +108: [20:24:14] ^ +108: [20:24:14] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [20:24:14] dasfsadf +108: [20:24:14] SMILES Parse Error: syntax error while parsing: --- +108: [20:24:14] SMILES Parse Error: check for mistakes around position 1: +108: [20:24:14] --- +108: [20:24:14] ^ +108: [20:24:14] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [20:24:14] dasfsadf +108: [20:24:14] SMILES Parse Error: syntax error while parsing: --- +108: [20:24:14] SMILES Parse Error: check for mistakes around position 1: +108: [20:24:14] --- +108: [20:24:14] ^ +108: [20:24:14] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [20:24:14] dasfsadf +108: [20:24:14] SMILES Parse Error: syntax error while parsing: --- +108: [20:24:14] SMILES Parse Error: check for mistakes around position 1: +108: [20:24:14] --- +108: [20:24:14] ^ +108: [20:24:14] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [20:24:14] dasfsadf +108: [20:24:14] SMILES Parse Error: syntax error while parsing: --- +108: [20:24:14] SMILES Parse Error: check for mistakes around position 1: +108: [20:24:14] --- +108: [20:24:14] ^ +108: [20:24:14] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [20:24:14] dasfsadf +108: [20:24:14] SMILES Parse Error: syntax error while parsing: --- +108: [20:24:14] SMILES Parse Error: check for mistakes around position 1: +108: [20:24:14] --- +108: [20:24:14] ^ +108: [20:24:14] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [20:24:14] dasfsadf +108: [20:24:14] SMILES Parse Error: syntax error while parsing: --- +108: [20:24:14] SMILES Parse Error: check for mistakes around position 1: +108: [20:24:14] --- +108: [20:24:14] ^ +108: [20:24:14] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [20:24:14] dasfsadf +147: [20:24:14] UFFTYPER: Unrecognized charge state for atom: 5 +108: [20:24:14] SMILES Parse Error: syntax error while parsing: --- +108: [20:24:14] SMILES Parse Error: check for mistakes around position 1: +108: [20:24:14] --- +108: [20:24:14] ^ +108: [20:24:14] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [20:24:14] dasfsadf +108: [20:24:14] SMILES Parse Error: syntax error while parsing: --- +108: [20:24:14] SMILES Parse Error: check for mistakes around position 1: +108: [20:24:14] --- +108: [20:24:14] ^ +108: [20:24:14] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [20:24:14] dasfsadf +108: [20:24:14] SMILES Parse Error: syntax error while parsing: --- +108: [20:24:14] SMILES Parse Error: check for mistakes around position 1: +108: [20:24:14] --- +108: [20:24:14] ^ +108: [20:24:14] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [20:24:14] dasfsadf +108: [20:24:14] SMILES Parse Error: syntax error while parsing: --- +108: [20:24:14] SMILES Parse Error: check for mistakes around position 1: +108: [20:24:14] --- +108: [20:24:14] ^ +108: [20:24:14] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [20:24:14] dasfsadf +159: file test2_1.png gave hash 240594419U not the expected 638584804U +69: [20:24:14] 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: [20:24:14] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +148: .[20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +125: Warning: Atom Count for residue LYS80A does not match expected count +160: Randomness seeded to: 1163177893 +160: file testAtomTags_3.svg gave hash 1931256064U not the expected 2244078420U +145: ... +145: ---------------------------------------------------------------------- +145: Ran 19 tests in 0.173s +145: +145: OK +159: file test2_2.png gave hash 278647755U not the expected 610424244U +161: file rxn_test1_1.png gave hash 760679292U not the expected 801892091U 68: Test 68: -68: BMS-986142_atrop5.mrv +68: mrtx1719_3d.mrv 68: -68: [00:24:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -68: [00:24:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -143: generating reference data -159: file test2_1.png gave hash 240594419U not the expected 638584804U 68: Test 68: -68: BMS-986142_atrop6.mrv +68: mrtx1719_atrop1.mrv 68: 68: Test 68: -68: BMS-986142_atrop7.mrv +68: mrtx1719_atrop2.mrv 68: 68: Test 68: -68: BMS-986142_atrop8.mrv +68: mrtx1719_atrop3.mrv 68: -68: [00:24:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -68: [00:24:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -145: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -159: file test2_2.png gave hash 278647755U not the expected 610424244U -145: [00:24:57] Molecule does not have explicit Hs. Consider calling AddHs() -145: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [00:24:57] Molecule does not have explicit Hs. Consider calling AddHs() -145: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [00:24:57] Molecule does not have explicit Hs. Consider calling AddHs() -145: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [00:24:57] Molecule does not have explicit Hs. Consider calling AddHs() -145: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [00:24:57] Molecule does not have explicit Hs. Consider calling AddHs() -145: ..[00:24:57] Molecule does not have explicit Hs. Consider calling AddHs() -161: file rxn_test1_1.png gave hash 760679292U not the expected 801892091U -145: [00:24:57] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [00:24:57] Molecule does not have explicit Hs. Consider calling AddHs() -160: file contourMol_1.svg gave hash 4125787245U not the expected 3634867913U 68: Test 68: -68: BMS-986142_atropBad2.mrv +68: mrtx1719_atropBad1.mrv 68: -89: [00:24:57] Explicit valence for atom # 3 Al, 6, is greater than permitted -68: [00:24:57] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +68: [20:24:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +148: ..[20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() 159: Done 159: ----------------- Test 4 -160: file contourMol_2.svg gave hash 4241964660U not the expected 1815941817U -145: .[00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [00:24:57] Molecule does not have explicit Hs. Consider calling AddHs() -69: [00:24:57] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas -69: [00:24:57] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' -147: [00:24:57] UFFTYPER: Unrecognized charge state for atom: 6 -147: [00:24:57] UFFTYPER: Unrecognized charge state for atom: 6 +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +147: [20:24:14] UFFTYPER: Unrecognized charge state for atom: 6 +142: done +148: ..[20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +124/236 Test #145: pyForceFieldHelpers .................... Passed 0.48 sec +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 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: -124/236 Test #60: cxsmilesTest ........................... Passed 1.49 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 -160: file contourMol_3.svg gave hash 1333854566U not the expected 2579392727U -160: file contourMol_4.svg gave hash 4249475618U not the expected 2914799663U -154: .[00:24:57] Molecule does not have explicit Hs. Consider calling AddHs() -147: [00:24:57] UFFTYPER: Unrecognized charge state for atom: 6 -145: .[00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [00:24:57] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [00:24:57] Molecule does not have explicit Hs. Consider calling AddHs() -108: .[00:24:57] SMILES Parse Error: syntax error while parsing: mydoghasfleas -108: [00:24:57] SMILES Parse Error: check for mistakes around position 1: -108: [00:24:57] mydoghasfleas -108: [00:24:57] ^ -108: [00:24:57] SMILES Parse Error: Failed parsing SMILES 'mydoghasfleas' for input: 'mydoghasfleas' +147: [20:24:14] UFFTYPER: Unrecognized charge state for atom: 6 +142: [20:24:14] done +148: .[20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +141: processing +141: launch :0 +141: launch :1 +141: launch :2 +141: launch :3 +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +161: file rxn_test1_2.png gave hash 3312211595U not the expected 507435337U +147: [20:24:14] UFFTYPER: Unrecognized charge state for atom: 6 +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() 159: file test5_1.png gave hash 650561118U not the expected 571291290U +160: file contourMol_1.svg gave hash 4125787245U not the expected 3634867913U +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +141: [20:24:14] Rep: 0 Mol:2 +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +130: [20:24:14] done +130: [20:24:14] ------------------------------------- +130: [20:24:14] Test Rooted Topological Torsions. +130: [20:24:14] done +130: [20:24:14] ------------------------------------- +130: [20:24:14] Test ignoring atoms in Topological Torsions. +130: [20:24:14] done +130: [20:24:14] ------------------------------------- +141: [20:24:14] Rep: 0 Mol:0 +130: [20:24:14] ------------------------------------- +130: [20:24:14] Test Topological Torsions including info about chirality. +130: [20:24:14] done +130: [20:24:14] ------------------------------------- +130: [20:24:14] Test GitHub Issue 25: fingerprint backwards compatibility. +130: [20:24:14] done +130: [20:24:14] ------------------------------------- +130: [20:24:14] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. +130: [20:24:14] done +130: [20:24:14] ------------------------------------- +130: [20:24:14] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +141: [20:24:14] Rep: 0 Mol:1 +125/236 Test #142: testMMFFForceFieldHelpersMultiThread ... Passed 0.59 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 +141: [20:24:14] Rep: 0 Mol:5 +141: [20:24:14] Rep: 0 Mol:3 +141: [20:24:14] Rep: 0 Mol:9 +141: [20:24:14] Rep: 0 Mol:4 +141: [20:24:14] Rep: 0 Mol:13 +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +69: ---------------------------------- +69: ---------------------------------- +69: [20:24:14] +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# 0x000055CD737F3FFF in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 4# 0x000055CD7384D3EA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 5# 0x000055CD737CD923 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 6# 0x00007FED99C33CA8 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# 0x000055CD737CDAD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: ---------- +69: **** +69: +69: [20:24:14] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +108: .[20:24:14] SMILES Parse Error: syntax error while parsing: mydoghasfleas +108: [20:24:14] SMILES Parse Error: check for mistakes around position 1: +108: [20:24:14] mydoghasfleas +108: [20:24:14] ^ +108: [20:24:14] SMILES Parse Error: Failed parsing SMILES 'mydoghasfleas' for input: 'mydoghasfleas' +130: [20:24:14] done +130: [20:24:14] ------------------------------------- +130: [20:24:14] Test convenience and bulk fp calculation functions +160: file contourMol_2.svg gave hash 4241964660U not the expected 1815941817U +143: processing +143: launch :0 +143: launch :1 +143: launch :2 +143: launch :3 +143: [20:24:14] Rep: 0 Mol:2 +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +159: file test5_2.png gave hash 2649140411U not the expected 97265124U +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +143: [20:24:14] Rep: 0 Mol:[20:24:14] Rep: 0 Mol:0 +143: [20:24:14] Rep: 0 Mol:3 +141: [20:24:14] Rep: 0 Mol:6 +141: [20:24:14] Rep: 0 Mol:10 +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +143: 1 +143: [20:24:14] Rep: 0 Mol:5 +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +141: [20:24:14] Rep: 0 Mol:17 +141: [20:24:14] Rep: 0 Mol:8 +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +154: .[20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +141: [20:24:14] Rep: 0 Mol:7 +141: [20:24:14] Rep: 0 Mol:11 +143: [20:24:14] Rep: 0 Mol:4 +143: [20:24:14] Rep: 0 Mol:9 +159: file test5_3.png gave hash 2951986966U not the expected 606188176U +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +148: [20:24:14] 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 @@ -27111,6 +27353,30 @@ 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 +141: [20:24:14] Rep: 0 Mol:15 +141: [20:24:14] Rep: 0 Mol:19 +158: . +158: ---------------------------------------------------------------------- +158: Ran 1 test in 0.012s +158: +158: OK +160: file contourMol_3.svg gave hash 1333854566U not the expected 2579392727U +159: Done +159: ----------------- Test 6 (atom labels) +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +154: .[20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +141: [20:24:14] Rep: 0 Mol:23 +141: [20:24:14] Rep: 0 Mol:12 +141: [20:24:14] Rep: 0 Mol:27 +143: [20:24:14] Rep: 0 Mol:6 +143: [20:24:14] Rep: 0 Mol:7 +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +143: [20:24:14] Rep: 0 Mol:13 +141: [20:24:14] Rep: 0 Mol:31 +141: [20:24:14] Rep: 0 Mol:16 +159: Done +159: ----------------- Test 7 (backgrounds) 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 @@ -27911,59 +28177,6 @@ 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_51_54554.txt 165: -148: .[00:24:57] Molecule does not have explicit Hs. Consider calling AddHs() -89: [00:24:57] Explicit valence for atom # 4 Al, 6, is greater than permitted -125/236 Test #133: pyTestGenerator ........................ Passed 0.73 sec -154: .[00:24:57] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [00:24:57] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [00:24:57] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[00:24:57] UFFTYPER: Unrecognized hybridization for atom: 0 -145: [00:24:57] UFFTYPER: Unrecognized atom type: Cu+1 (0) -145: .[00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [00:24:57] Molecule does not have explicit Hs. Consider calling AddHs() -145: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [00:24:57] Molecule does not have explicit Hs. Consider calling AddHs() -145: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [00:24:57] Molecule does not have explicit Hs. Consider calling AddHs() -145: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [00:24:57] Molecule does not have explicit Hs. Consider calling AddHs() -145: [00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [00:24:57] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [00:24:57] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[00:24:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [00:24:57] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[00:24:57] Molecule does not have explicit Hs. Consider calling AddHs() -145: [00:24:57] Molecule does not have explicit Hs. Consider calling AddHs() -145: ...[00:24:57] Molecule does not have explicit Hs. Consider calling AddHs() -145: [00:24:57] Molecule does not have explicit Hs. Consider calling AddHs() -145: [00:24:57] Molecule does not have explicit Hs. Consider calling AddHs() -108: ....... -108: ---------------------------------------------------------------------- -108: Ran 21 tests in 0.926s -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 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 @@ -28230,228 +28443,324 @@ 165: 165: testFileSDF_RandomSet(): benchmark/chembl13_threshold_90.smi 165: ERROR: RDKit could not load input file -126/236 Test #165: FMCStest ............................... Passed 0.18 sec -148: [00:24:57] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:24:57] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:24:57] Molecule does not have explicit Hs. Consider calling AddHs() -148: ..[00:24:57] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:24:57] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:24:57] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:24:57] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:24:57] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:24:57] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:24:57] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:24:57] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:24:57] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:24:57] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:24:57] Molecule does not have explicit Hs. Consider calling AddHs() -148: ..[00:24:57] Molecule does not have explicit Hs. Consider calling AddHs() -148: .[00:24:57] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:24:57] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:24:57] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:24:57] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:24:57] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:24:57] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:24:57] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:24:57] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:24:57] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:24:57] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:24:58] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:24:58] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:24:58] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:24:58] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:24:58] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:24:58] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:24:58] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:24:58] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:24:58] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:24:58] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:24:58] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:24:58] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:24:58] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:24:58] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:24:58] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:24:58] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:24:58] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:24:58] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:24:58] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:24:58] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:24:58] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:24:58] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:24:58] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:24:58] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:24:58] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:24:58] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:24:58] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:24:58] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:24:58] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:24:58] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:24:58] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:24:58] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:24:58] Molecule does not have explicit Hs. Consider calling AddHs() -89: [00:24:57] Explicit valence for atom # 10 Si, 6, is greater than permitted +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +143: [20:24:14] Rep: 0 Mol:10 +143: [20:24:14] Rep: 0 Mol:11 +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +143: [20:24:14] Rep: 0 Mol:15 +143: [20:24:14] Rep: 0 Mol:19 +161: file rxn_test1_3.png gave hash 288594716U not the expected 1590809137U +126/236 Test #165: FMCStest ............................... Passed 0.07 sec +160: file contourMol_4.svg gave hash 4249475618U not the expected 2914799663U +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 +160: file contourMol_5.svg gave hash 3954963517U not the expected 3792684719U +141: [20:24:14] Rep: 0 Mol:14 +141: [20:24:14] Rep: 0 Mol:18 +141: [20:24:14] Rep: 0 Mol:20 +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +143: [20:24:14] Rep: 0 Mol:23 +143: [20:24:14] Rep: 0 Mol:27 +143: [20:24:14] Rep: 0 Mol:17 +143: [20:24:14] Rep: 0 Mol:31 +143: [20:24:14] Rep: 0 Mol:8 +161: file rxn_test1_4.png gave hash 1996676260U not the expected 1766700542U +159: file test7_1.png gave hash 2406197059U not the expected 1322246680U +141: [20:24:14] Rep: 0 Mol:21 +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +127/236 Test #158: pyMolCatalog ........................... Passed 0.35 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: [20:24:14] Rep: 0 Mol:22 +141: [20:24:14] Rep: 0 Mol:25 +141: [20:24:14] Rep: 0 Mol:24 68: Test 68: -68: JDQ443_3d.mrv +68: AlexRxn.mrv 68: 68: Test 68: -68: JDQ443_atrop1.mrv +68: BadReactionSign.mrv 68: 68: Test 68: -68: JDQ443_atrop2.mrv +68: bondArray_node.mrv 68: 68: Test 68: -68: JDQ443_atrop3.mrv +68: marvin03.mrv 68: 68: Test 68: -68: JDQ443_atropBad1.mrv +68: marvin04.mrv 68: -68: [00:24:57] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 68: Test 68: -68: RP-6306_atrop1.mrv +68: marvin08.mrv 68: 68: Test 68: -68: RP-6306_atrop2.mrv +68: marvin09.mrv 68: 68: Test 68: -68: RP-6306_atrop3.mrv +68: marvin11.mrv 68: 68: Test 68: -68: RP-6306_atrop4.mrv +68: marvin05.mrv 68: 68: Test 68: -68: RP-6306_atrop5.mrv +68: EmptyRxn.mrv 68: -68: [00:24:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -68: [00:24:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +68: [20:24:14] initialization failed +143: [20:24:14] Rep: 0 Mol:14 +143: [20:24:14] Rep: 0 Mol:18 +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +161: file rxn_test1_5.png gave hash 1068409486U not the expected 2552100594U +141: [20:24:14] Rep: 0 Mol:26 +126: Warning: Atom Count for residue ASN39A does not match expected count +143: [20:24:14] Rep: 0 Mol:12 +143: [20:24:14] Rep: 0 Mol:16 +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +143: [20:24:14] Rep: 0 Mol:22 +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 +141: [20:24:14] Rep: 0 Mol:29 +117: =>start test morse custom +117: [20:24:14] test on : 365 molecules done +143: [20:24:14] Rep: 0 Mol:26 +141: [20:24:14] Rep: 0 Mol:28 +141: [20:24:14] Rep: 0 Mol:30 +143: [20:24:14] Rep: 0 Mol:20 +143: [20:24:14] Rep: 0 Mol:30 +143: [20:24:14] Rep: 0 Mol:21 +161: file rxn_test1_6.png gave hash 1112775934U not the expected 3791582903U +143: [20:24:14] Rep: 0 Mol:24 +143: [20:24:14] Rep: 0 Mol:25 +143: [20:24:14] Rep: 0 Mol:28 +143: [20:24:14] Rep: 0 Mol:29 +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +161: file rxn_test1_7.png gave hash 1360101162U not the expected 1461397406U +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 +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +159: generating reference drawings +108: ....... +108: ---------------------------------------------------------------------- +108: Ran 21 tests in 1.086s +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 +154: ..[20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +154: .[20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +154: .[20:24:14] SMARTS Parse Error: syntax error while parsing: [N,O;!HQ] +154: [20:24:14] SMARTS Parse Error: Failed parsing SMARTS '[N,O;!HQ]' for input: '[N,O;!HQ]' +154: ... +154: ---------------------------------------------------------------------- +154: Ran 9 tests in 0.165s +154: +154: OK +141: [20:24:14] Rep: 20 Mol:3 +141: [20:24:14] Rep: 20 Mol:7 +141: [20:24:14] Rep: 20 Mol:11 +141: [20:24:14] Rep: 20 Mol:15 +166: Randomness seeded to: 2696818778 +166: =============================================================================== +166: All tests passed (363 assertions in 14 test cases) +166: +141: [20:24:14] Rep: 20 Mol:19 +141: [20:24:14] Rep: 20 Mol:23 +128/236 Test #166: molHashCatchTest ....................... Passed 0.14 sec +141: [20:24:14] Rep: 20 Mol:27 +141: [20:24:14] Rep: 20 Mol:31 +141: [20:24:14] Rep: 20 Mol:1 +141: [20:24:14] Rep: 20 Mol:5 +141: [20:24:14] Rep: 20 Mol:9 +141: [20:24:14] Rep: 20 Mol:13 +141: [20:24:14] Rep: 20 Mol:17 +141: [20:24:14] Rep: 20 Mol:21 +141: [20:24:14] Rep: 20 Mol:25 +141: [20:24:14] Rep: 20 Mol:29 +141: [20:24:14] Rep: 20 Mol:0 +141: [20:24:14] Rep: 20 Mol:4 +141: [20:24:14] Rep: 20 Mol:8 +141: [20:24:14] Rep: 20 Mol:12 +141: [20:24:14] Rep: 20 Mol:16 +141: [20:24:14] Rep: 20 Mol:20 +141: [20:24:14] Rep: 20 Mol:24 +141: [20:24:14] Rep: 20 Mol:28 +141: [20:24:14] Rep: 40 Mol:3 +141: [20:24:14] Rep: 40 Mol:7 +141: [20:24:14] Rep: 40 Mol:11 +141: [20:24:14] Rep: 40 Mol:15 +141: [20:24:14] Rep: 40 Mol:19 +141: [20:24:14] Rep: 40 Mol:23 +141: [20:24:14] Rep: 40 Mol:27 +141: [20:24:14] Rep: 40 Mol:31 +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +126: Warning: Atom Count for residue GLU53A does not match expected count +126: Warning: Atom Count for residue ARG64A does not match expected count 68: Test 68: -68: RP-6306_atropBad1.mrv +68: RxnNoCoords.mrv 68: -68: [00:24:57] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 68: Test 68: -68: RP-6306_atropBad2.mrv +68: mrvValenceZero.mrv 68: -68: [00:24:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -68: [00:24:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -68: [00:24:57] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -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 -156: . -156: ---------------------------------------------------------------------- -156: Ran 1 test in 0.062s -156: -156: OK -156: Testing Shape Helpers wrapper -154: ..[00:24:58] Molecule does not have explicit Hs. Consider calling AddHs() -154: .[00:24:58] Molecule does not have explicit Hs. Consider calling AddHs() -154: .[00:24:58] SMARTS Parse Error: syntax error while parsing: [N,O;!HQ] -154: [00:24:58] SMARTS Parse Error: Failed parsing SMARTS '[N,O;!HQ]' for input: '[N,O;!HQ]' -154: ... -154: ---------------------------------------------------------------------- -154: Ran 9 tests in 0.138s -154: -154: OK -145: ... -145: ---------------------------------------------------------------------- -145: Ran 19 tests in 0.163s -145: -145: OK 68: Test 68: -68: RP-6306_3d.mrv +68: condition_coordinates_mpoint.mrv 68: 68: Test 68: -68: Sotorasib_atrop1.mrv +68: marvin01.mrv 68: 68: Test 68: -68: Sotorasib_atrop2.mrv +68: aspirineSynthesisWithAttributes.mrv 68: 68: Test 68: -68: Sotorasib_atrop3.mrv +68: marvin01.mrv 68: 68: Test 68: -68: Sotorasib_atrop4.mrv +68: NewChiralTest 68: 68: Test 68: -68: Sotorasib_atrop5.mrv +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: [00:24:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -68: [00:24:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +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: +156: . +156: ---------------------------------------------------------------------- +156: Ran 1 test in 0.237s +156: +156: OK +156: Testing Shape Helpers wrapper +159: processing +159: launch :0 +159: launch :1 +159: launch :2 +159: launch :3 +69: [20:24:14] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas +69: [20:24:14] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' +69: [20:24:14] Empty atom list: 'M ALS 1 0 F' on line 8. +69: de_DE.UTF-8 +69: [20:24:14] ------------------------------------- +69: [20:24:14] Test multithreading Locale Switching 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 -125: Warning: Atom Count for residue LYS80A does not match expected count -160: file contourMol_5.svg gave hash 3954963517U not the expected 3792684719U -126: Warning: Atom Count for residue ASN39A does not match expected count -166: Randomness seeded to: 581442070 -166: =============================================================================== -166: All tests passed (363 assertions in 14 test cases) -166: -158: . -158: ---------------------------------------------------------------------- -158: Ran 1 test in 0.015s -158: -158: OK -141: processing -141: launch :0 -141: launch :1 -141: [00:24:58] Rep: 0 Mol:0 -141: [00:24:58] Rep: 0 Mol:1 -141: launch :2 -141: launch :3 -141: [00:24:58] Rep: 0 Mol:2 -141: [00:24:58] Rep: 0 Mol:3 -141: [00:24:58] Rep: 0 Mol:5 -141: [00:24:58] Rep: 0 Mol:9 -141: [00:24:58] Rep: 0 Mol:13 -141: [00:24:58] Rep: 0 Mol:4 -141: [00:24:58] Rep: 0 Mol:17 -141: [00:24:58] Rep: 0 Mol:6 -141: [00:24:58] Rep: 0 Mol:10 -141: [00:24:58] Rep: 0 Mol:8 -141: [00:24:58] Rep: 0 Mol:12 -141: [00:24:58] Rep: 0 Mol:16 -141: [00:24:58] Rep: 0 Mol:21 -141: [00:24:58] Rep: 0 Mol:25 -161: file rxn_test1_2.png gave hash 3312211595U not the expected 507435337U -69: [00:24:58] Empty atom list: 'M ALS 1 0 F' on line 8. -69: de_DE.UTF-8 -69: [00:24:58] ------------------------------------- -69: [00:24:58] Test multithreading Locale Switching -127/236 Test #108: pyFilterCatalog ........................ Passed 1.36 sec -128/236 Test #145: pyForceFieldHelpers .................... Passed 0.65 sec -129/236 Test #154: pyChemicalFeatures ..................... Passed 0.50 sec -130/236 Test #156: pyShapeHelpers ......................... Passed 0.47 sec -131/236 Test #158: pyMolCatalog ........................... Passed 0.43 sec -132/236 Test #166: molHashCatchTest ....................... Passed 0.20 sec -68: Test -68: -68: Sotorasib_atropBad1.mrv -68: -68: [00:24:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +129/236 Test #68: testMrvToMol ........................... Passed 1.85 sec +130/236 Test #108: pyFilterCatalog ........................ Passed 1.59 sec +131/236 Test #154: pyChemicalFeatures ..................... Passed 0.71 sec +132/236 Test #156: pyShapeHelpers ......................... Passed 0.68 sec test 169 Start 169: pyMMPA @@ -28476,71 +28785,31 @@ 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 -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 -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 -141: [00:24:58] Rep: 0 Mol:20 -141: [00:24:58] Rep: 0 Mol:29 -141: [00:24:58] Rep: 0 Mol:24 -141: [00:24:58] Rep: 0 Mol:7 -141: [00:24:58] Rep: 0 Mol:28 -141: [00:24:58] Rep: 0 Mol:11 -141: [00:24:58] Rep: 0 Mol:15 -141: [00:24:58] Rep: 0 Mol:19 -141: [00:24:58] Rep: 0 Mol:14 -141: [00:24:58] Rep: 0 Mol:23 -141: [00:24:58] Rep: 0 Mol:27 -141: [00:24:58] Rep: 0 Mol:31 -159: file test5_2.png gave hash 2649140411U not the expected 97265124U -159: file test5_3.png gave hash 2951986966U not the expected 606188176U -159: Done -159: ----------------- Test 6 (atom labels) -159: Done -159: ----------------- Test 7 (backgrounds) -130: [00:24:58] done -130: [00:24:58] ------------------------------------- -130: [00:24:58] Test GitHub Issue #6958 -130: [00:24:58] DEPRECATION WARNING: please use AtomPairGenerator -148: [00:24:58] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:24:58] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:24:58] Molecule does not have explicit Hs. Consider calling AddHs() -68: Test -68: -68: Sotorasib_atropBad2.mrv -68: -68: [00:24:58] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -89: [00:24:58] Explicit valence for atom # 2 O, 4, is greater than permitted -89: [00:24:58] Explicit valence for atom # 3 Al, 6, is greater than permitted -89: [00:24:58] Explicit valence for atom # 3 Be, 4, is greater than permitted -69: [00:24:58] Test multithreading (Done) -69: [00:24:58] ------------------------------------- -69: *************************************** -69: *************************************** -69: [00:24:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: [00:24:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -126: Warning: Atom Count for residue GLU53A does not match expected count -161: file rxn_test1_3.png gave hash 288594716U not the expected 1590809137U -133/236 Test #130: testFingerprintGenerators .............. Passed 1.00 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 -162: ...[00:24:58] Font file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/Amadeus.ttf not found. -162: [00:24:58] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +167: .... +167: ---------------------------------------------------------------------- +167: Ran 4 tests in 0.015s +167: +167: OK +161: file rxn_test2_1.png gave hash 3339775168U not the expected 3551633840U +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 +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +141: [20:24:14] Rep: 20 Mol:2 +141: [20:24:14] Rep: 20 Mol:6 +141: [20:24:14] Rep: 20 Mol:10 +141: [20:24:14] Rep: 20 Mol:14 +141: [20:24:14] Rep: 20 Mol:18 +141: [20:24:14] Rep: 20 Mol:22 +160: file testGithub3226_1.png gave hash 2093087177U not the expected 3165135374U +133/236 Test #167: pyMolHash .............................. Passed 0.36 sec +162: ...[20:24:14] Font file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/Amadeus.ttf not found. +162: [20:24:14] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +141: [20:24:14] Rep: 20 Mol:26 +141: [20:24:14] Rep: 20 Mol:30 +160: file testGithub3226_2.png gave hash 228776032U not the expected 643975155U 168: 168: TEST mol: Case1 Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1 Case1 -168: Time elapsed 0.005196 seconds +168: Time elapsed 0.013567 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. 168: 2: res= c1ccc([*:2])c([*:1])c1,C[*:1].C[C:3](C(=O)N[*:2])[NH+]1CCCC1 @@ -28553,55 +28822,27 @@ 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] 168: 6: NOREF. Reference data NOT LISTED in test case. -159: file test7_1.png gave hash 2406197059U not the expected 1322246680U -141: [00:24:58] Rep: 0 Mol:18 168: 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. +161: file rxn_test2_2_1.png gave hash 457778262U not the expected 1268122583U +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 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. 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. -143: processing -143: launch :0 -143: launch :1 -143: launch :2 -143: launch :3 -143: [00:24:58] Rep: 0 Mol:2 -143: [00:24:58] Rep: 0 Mol:3 -69: [00:24:58] bond with order 0 found on line 7. This is not part of the MDL specification. -148: [00:24:58] 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: [00:24:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -143: [00:24:58] Rep: 0 Mol:0 -143: [00:24:58] Rep: 0 Mol:1 168: 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. -143: [00:24:58] Rep: 0 Mol:5 168: 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. 168: 15: res= C[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.Cc1ccccc1NC(=O)[*:1] @@ -28612,145 +28853,49 @@ 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: [00:24:58] Rep: 0 Mol:4 -143: [00:24:58] Rep: 0 Mol:9 -89: [00:24:58] Explicit valence for atom # 27 P, 6, is greater than permitted -141: [00:24:58] Rep: 0 Mol:22 -161: file rxn_test1_4.png gave hash 1996676260U not the expected 1766700542U -148: [00:24:58] Molecule does not have explicit Hs. Consider calling AddHs() -69: [00:24:58] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) -69: [00:24:58] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) -69: [00:24:58] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -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: [00:24:58] Rep: 0 Mol:7 -143: [00:24:58] Rep: 0 Mol:11 -143: [00:24:58] Rep: 0 Mol:6 -143: [00:24:58] Rep: 0 Mol:13 -143: [00:24:58] Rep: 0 Mol:15 -143: [00:24:58] Rep: 0 Mol:10 -141: [00:24:58] Rep: 0 Mol:26 -148: [00:24:58] Molecule does not have explicit Hs. Consider calling AddHs() -69: generating smiles -162: ..........[00:24:58] -162: -162: **** -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 -143: [00:24:58] Rep: 0 Mol:19 -162: Pre-condition Violation -162: molecule must not be None -162: Violation occurred on line 432 in file ./Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp -162: Failed Expression: m -162: ---------- -162: Stacktrace: -162: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -162: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -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# 0x00007F92A00B862C 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 -162: 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 -162: 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 -162: 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 -162: 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/rdmolfiles.so -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# 0x00007F929E5B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -162: 17# 0x00007F929E5B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -162: 18# 0x00007F929E5B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -162: 19# 0x00007F929E5B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -162: 20# 0x00007F929E5B7933 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# 0x00007F92A00B53C6 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 -162: 30# _PyEval_EvalFrameDefault in /usr/bin/python3 -162: 31# 0x0000000000690C6F in /usr/bin/python3 -162: 32# 0x000000000062D590 in /usr/bin/python3 -162: 33# _PyObject_MakeTpCall in /usr/bin/python3 -162: 34# _PyEval_EvalFrameDefault in /usr/bin/python3 -162: 35# 0x00000000005CD3C9 in /usr/bin/python3 -162: 36# _PyEval_EvalFrameDefault in /usr/bin/python3 -162: 37# 0x0000000000690C6F in /usr/bin/python3 -162: 38# 0x000000000062D590 in /usr/bin/python3 -162: 39# _PyObject_MakeTpCall in /usr/bin/python3 -162: 40# _PyEval_EvalFrameDefault in /usr/bin/python3 -162: 41# 0x00000000005CD3C9 in /usr/bin/python3 -162: 42# _PyEval_EvalFrameDefault in /usr/bin/python3 -162: 43# 0x0000000000690C6F in /usr/bin/python3 -162: 44# 0x000000000062D590 in /usr/bin/python3 -162: 45# _PyObject_MakeTpCall in /usr/bin/python3 -162: 46# _PyEval_EvalFrameDefault in /usr/bin/python3 -162: 47# 0x00000000005A090C in /usr/bin/python3 -162: 48# _PyObject_MakeTpCall in /usr/bin/python3 -162: 49# _PyEval_EvalFrameDefault in /usr/bin/python3 -162: 50# PyEval_EvalCode in /usr/bin/python3 -162: 51# 0x00000000006AB8D1 in /usr/bin/python3 -162: 52# 0x00000000006A899C in /usr/bin/python3 -162: 53# 0x00000000006B9943 in /usr/bin/python3 -162: 54# 0x00000000006B93E3 in /usr/bin/python3 -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# 0x00007F92A12DDCA8 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: -143: [00:24:58] Rep: 0 Mol:23 -143: [00:24:58] Rep: 0 Mol:27 +148: [20:24:14] 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>>[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 +141: [20:24:14] Rep: 40 Mol:0 +141: [20:24:14] [20:24:14] Rep: 60 Mol:3 +141: Rep: 40 Mol:4 +141: [20:24:14] Rep: 40 Mol:8 +141: [20:24:14] Rep: 40 Mol:12 +141: [20:24:14] Rep: 40 Mol:16 +126: Warning: Atom Count for residue LYS80A does not match expected count +160: file testGithub3226_3.png gave hash 1938488947U not the expected 3119571946U +141: [20:24:14] Rep: 60 Mol:7 +141: [20:24:14] Rep: 60 Mol:11 +141: [20:24:14] Rep: 60 Mol:15 +141: [20:24:14] Rep: 60 Mol:19 +141: [20:24:14] Rep: 60 Mol:23 +141: [20:24:14] Rep: 60 Mol:27 +141: [20:24:14] Rep: 60 Mol:31 +161: file rxn_test2_2_2.png gave hash 4285088210U not the expected 82821108U 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 0.008462 seconds +168: Time elapsed 0.008777 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 168: 1: PASSED. matchedRefRes = 4 168: 2: O=[n+]1c([*:2])c([*:1])n([O-])c2ccccc21, C[*:1].O=C(NCCO)[*:2] 168: 2: PASSED. matchedRefRes = 1 -126: Warning: Atom Count for residue ARG64A does not match expected count -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: [00:24:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 168: 3: O=C(N[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O, C[*:1].OCC[*:2] 168: 3: PASSED. matchedRefRes = 6 -69: check isomorphism -143: [00:24:58] Rep: 0 Mol:31 +117: =>start test AUTOCORR3D custom +117: [20:24:14] test on : 365 molecules done +141: [20:24:14] Rep: 40 Mol:1 +141: [20:24:14] Rep: 40 Mol:5 +141: [20:24:14] Rep: 40 Mol:9 +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +141: [20:24:14] Rep: 40 Mol:13 +141: [20:24:14] Rep: 40 Mol:20 +141: [20:24:14] Rep: 40 Mol:17 +141: [20:24:14] Rep: 40 Mol:24 +141: [20:24:14] Rep: 40 Mol:28 +141: [20:24:14] Rep: 40 Mol:21 168: 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] @@ -28759,8 +28904,6 @@ 168: 6: PASSED. matchedRefRes = 10 168: 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] -143: [00:24:58] Rep: 0 Mol:17 -141: [00:24:58] Rep: 0 Mol:30 168: 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] @@ -28771,24 +28914,18 @@ 168: 11: NOREF. Reference data NOT LISTED in test case.C([*:1])[*:2],Cc1c(C(=O)N[*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] 168: 12: C(C[*:2])[*:1], Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].O[*:2] 168: 12: PASSED. matchedRefRes = 8 -143: [00:24:58] Rep: 0 Mol:8 +141: [20:24:14] Rep: 40 Mol:25 168: 13: NULL, Cc1c(C(=O)NC[*:1])[n+](=O)c2ccccc2n1[O-].OC[*:1] 168: 13: PASSED. matchedRefRes = 9 168: 14: C([*:1])[*:2], Cc1c(C(=O)NC[*:1])[n+](=O)c2ccccc2n1[O-].O[*:2] 168: 14: PASSED. matchedRefRes = 11 168: 15: NULL, Cc1c(C(=O)NCC[*:1])[n+](=O)c2ccccc2n1[O-].O[*:1] 168: 15: PASSED. matchedRefRes = 2 -161: file rxn_test1_5.png gave hash 1068409486U not the expected 2552100594U -175: Randomness seeded to: 1534340228 -175: [00:24:58] non kekulizable aromatic bond being treated as bond order 1 -175: [00:24:58] non kekulizable aromatic bond being treated as bond order 1 -175: [00:24:58] non kekulizable aromatic bond being treated as bond order 1 -175: [00:24:58] non kekulizable aromatic bond being treated as bond order 1 -175: [00:24:58] non kekulizable aromatic bond being treated as bond order 1 -175: [00:24:58] non kekulizable aromatic bond being treated as bond order 1 -143: [00:24:58] Rep: 0 Mol:12 -143: [00:24:58] Rep: 0 Mol:16 -143: [00:24:58] Rep: 0 Mol:14 +160: file testPNGMetadata_1.png gave hash 3033029091U not the expected 997629701U +141: [20:24:14] Rep: 40 Mol:29 +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: 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] @@ -28798,12 +28935,11 @@ 168: ----------------------------------- 168: 168: TEST mol: ZINC21984717 Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-] ZINC21984717 -168: Time elapsed 0.004992 seconds +168: Time elapsed 0.004883 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: [00:24:58] Rep: 0 Mol:21 168: 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] @@ -28814,40 +28950,34 @@ 168: 6: PASSED. matchedRefRes = 10 168: 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. -143: [00:24:58] Rep: 0 Mol:20 -148: [00:24:58] Molecule does not have explicit Hs. Consider calling AddHs() 168: 8: res= O=C(NC[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] 168: 8: NOREF. Reference data NOT LISTED in test case. -143: [00:24:58] Rep: 0 Mol:18 -89: =============================================================================== -89: All tests passed (21562 assertions in 3 test cases) -89: -159: generating reference drawings -143: [00:24:58] Rep: 0 Mol:25 168: 9: res= O=C(NCC[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].O[*:1] 168: 9: NOREF. Reference data NOT LISTED in test case. +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() 168: 10: res= NULL,Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].OCC[*:1] 168: 10: PASSED. matchedRefRes = 3 168: 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] 168: 12: PASSED. matchedRefRes = 8 -134/236 Test #89: multithreadedSupplierCatchTest ......... Passed 1.63 sec 168: 13: res= NULL,Cc1c(C(=O)NC[*:1])[n+](=O)c2ccccc2n1[O-].OC[*:1] 168: 13: PASSED. matchedRefRes = 9 -test 176 - Start 176: pyCIPLabelsWrapTest +130: [20:24:14] done +130: [20:24:14] ------------------------------------- +130: [20:24:14] Test GitHub Issue #6958 +130: [20:24:14] DEPRECATION WARNING: please use AtomPairGenerator +134/236 Test #130: testFingerprintGenerators .............. Passed 1.37 sec +test 174 + Start 174: testSynthonSpaceRascalSearch -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 +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 168: 14: res= C([*:1])[*:2],Cc1c(C(=O)NC[*:1])[n+](=O)c2ccccc2n1[O-].O[*:2] 168: 14: PASSED. matchedRefRes = 11 168: 15: res= NULL,Cc1c(C(=O)NCC[*:1])[n+](=O)c2ccccc2n1[O-].O[*:1] 168: 15: PASSED. matchedRefRes = 2 -143: [00:24:58] Rep: 0 Mol:24 -143: [00:24:58] Rep: 0 Mol:22 -148: [00:24:58] Molecule does not have explicit Hs. Consider calling AddHs() 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] @@ -28857,12 +28987,9 @@ 168: ----------------------------------- 168: 168: TEST mol: Case1-SIMPLE CC(N1CC1)C(=O) Case1-SIMPLE -168: Time elapsed 0.001180 seconds +168: Time elapsed 0.001378 seconds 168: 1: res= NULL,C[*:1].O=CC(N1CC1)[*:1] 168: 1: PASSED. matchedRefRes = 2 -143: [00:24:58] Rep: 0 Mol:26 -143: [00:24:58] Rep: 0 Mol:28 -143: [00:24:58] Rep: 0 Mol:29 168: 2: res= O=CC([*:1])[*:2],C1CN1[*:2].C[*:1] 168: 2: PASSED. matchedRefRes = 3 168: 3: res= C([*:1])([*:2])[*:3],C1CN1[*:3].C[*:1].O=C[*:2] @@ -28875,7 +29002,6 @@ 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 -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] @@ -28883,7 +29009,7 @@ 168: ----------------------------------- 168: 168: TEST mol: Case1 Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1 Case1 -168: Time elapsed 0.005153 seconds +168: Time elapsed 0.005028 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. 168: 2: res= c1ccc([*:2])c([*:1])c1,C[*:1].C[C:3](C(=O)N[*:2])[NH+]1CCCC1 @@ -28892,7 +29018,6 @@ 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: file rxn_test1_6.png gave hash 1112775934U not the expected 3791582903U 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] @@ -28905,23 +29030,133 @@ 168: 9: NOREF. Reference data NOT LISTED in test case. 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. +69: [20:24:14] Test multithreading (Done) +69: [20:24:14] ------------------------------------- +162: ..........[20:24:14] +162: +162: **** +162: Pre-condition Violation +162: molecule must not be None +162: Violation occurred on line 432 in file ./Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp +162: Failed Expression: m +162: ---------- +162: Stacktrace: +162: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +162: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +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# 0x00007F6B8D7DF62C 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 +162: 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 +162: 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 +162: 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 +162: 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/rdmolfiles.so +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# 0x00007F6B8C3B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +162: 17# 0x00007F6B8C3B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +162: 18# 0x00007F6B8C3B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +162: 19# 0x00007F6B8C3B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +162: 20# 0x00007F6B8C3B7933 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# 0x00007F6B8D7DC3C6 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 +162: 30# _PyEval_EvalFrameDefault in /usr/bin/python3 +162: 31# 0x0000000000690C6F in /usr/bin/python3 +162: 32# 0x000000000062D590 in /usr/bin/python3 +162: 33# _PyObject_MakeTpCall in /usr/bin/python3 +162: 34# _PyEval_EvalFrameDefault in /usr/bin/python3 +162: 35# 0x00000000005CD3C9 in /usr/bin/python3 +162: 36# _PyEval_EvalFrameDefault in /usr/bin/python3 +162: 37# 0x0000000000690C6F in /usr/bin/python3 +162: 38# 0x000000000062D590 in /usr/bin/python3 +162: 39# _PyObject_MakeTpCall in /usr/bin/python3 +162: 40# _PyEval_EvalFrameDefault in /usr/bin/python3 +162: 41# 0x00000000005CD3C9 in /usr/bin/python3 +162: 42# _PyEval_EvalFrameDefault in /usr/bin/python3 +162: 43# 0x0000000000690C6F in /usr/bin/python3 +162: 44# 0x000000000062D590 in /usr/bin/python3 +162: 45# _PyObject_MakeTpCall in /usr/bin/python3 +162: 46# _PyEval_EvalFrameDefault in /usr/bin/python3 +162: 47# 0x00000000005A090C in /usr/bin/python3 +162: 48# _PyObject_MakeTpCall in /usr/bin/python3 +162: 49# _PyEval_EvalFrameDefault in /usr/bin/python3 +162: 50# PyEval_EvalCode in /usr/bin/python3 +162: 51# 0x00000000006AB8D1 in /usr/bin/python3 +162: 52# 0x00000000006A899C in /usr/bin/python3 +162: 53# 0x00000000006B9943 in /usr/bin/python3 +162: 54# 0x00000000006B93E3 in /usr/bin/python3 +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# 0x00007F6B8EF6ACA8 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: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +161: file rxn_test2_2_3.png gave hash 660865433U not the expected 3828365604U 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. +69: *************************************** +69: *************************************** +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: 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. -143: [00:24:58] Rep: 0 Mol:30 +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 +135/236 Test #60: cxsmilesTest ........................... Passed 2.08 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 +69: [20:24:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [20:24:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [20:24:14] bond with order 0 found on line 7. This is not part of the MDL specification. 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] 168: 16: NOREF. Reference data NOT LISTED in test case. -160: file testGithub3226_2.png gave hash 228776032U not the expected 643975155U 168: 17: res= Cc1ccccc1NC(=O)[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1] 168: 17: NOREF. Reference data NOT LISTED in test case. -148: [00:24:58] Molecule does not have explicit Hs. Consider calling AddHs() 168: 18: res= NULL,C1CC[NH+]([*:1])C1.Cc1ccccc1NC(=O)[C:2](C)[*:1] 168: 18: NOREF. Reference data NOT LISTED in test case. 168: @@ -28930,52 +29165,9 @@ 168: ----------------------------------- 168: 168: TEST mol: Case2 O=C(OCc1ccccc1)C(O)c1ccccc1 Case2 -168: Time elapsed 0.005344 seconds +168: Time elapsed 0.007486 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. -160: file testGithub3226_3.png gave hash 1938488947U not the expected 3119571946U -148: [00:24:58] Molecule does not have explicit Hs. Consider calling AddHs() -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: [00:24:58] initialization failed 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. 168: 3: res= O=C(O[*:2])[*:1],OC(c1ccccc1)[*:1].c1ccc(C[*:2])cc1 @@ -28992,26 +29184,24 @@ 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 testPNGMetadata_2.png gave hash 2637596984U not the expected 1797853056U +125: Warning: Atom Count for residue GLU150A does not match expected count +161: file rxn_test2_2_4.png gave hash 1904681261U not the expected 1230108677U +148: [20:24:14] 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. 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. -160: file testPNGMetadata_1.png gave hash 3033029091U not the expected 997629701U 168: 13: res= c1ccc(C([*:1])[*:2])cc1,O=C(OCc1ccccc1)[*:1].O[*:2] 168: 13: NOREF. Reference data NOT LISTED in test case. -148: [00:24:58] Molecule does not have explicit Hs. Consider calling AddHs() -141: [00:24:58] Rep: 20 Mol:1 -141: [00:24:58] Rep: 20 Mol:5 +161: Done +161: ----------------- Test 3: test reactant highlighting 168: 14: res= C([*:1])([*:2])[*:3],O=C(OCc1ccccc1)[*:1].O[*:2].c1ccc([*:3])cc1 168: 14: PASSED. matchedRefRes = 1 168: 15: res= OC([*:1])[*:2],O=C(OCc1ccccc1)[*:1].c1ccc([*:2])cc1 168: 15: NOREF. Reference data NOT LISTED in test case. -141: [00:24:58] Rep: 20 Mol:9 -141: [00:24:58] Rep: 20 Mol:13 -141: [00:24:58] Rep: 20 Mol:17 -141: [00:24:58] Rep: 20 Mol:21 168: 16: res= NULL,O=C(OCc1ccccc1)C(c1ccccc1)[*:1].O[*:1] 168: 16: NOREF. Reference data NOT LISTED in test case. 168: 17: res= O=C(OCc1ccccc1)C([*:1])[*:2],O[*:1].c1ccc([*:2])cc1 @@ -29022,383 +29212,320 @@ 168: --- ALL PASSED --- 168: ----------------------------------- 168: 5 TEST CASES FAILED -135/236 Test #168: testMMPA ............................... Passed 0.27 sec +136/236 Test #168: testMMPA ............................... Passed 0.26 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 +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +69: [20:24:14] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) +69: [20:24:14] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) +69: [20:24:14] 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: Randomness seeded to: 2858879707 +175: [20:24:14] non kekulizable aromatic bond being treated as bond order 1 +175: [20:24:14] non kekulizable aromatic bond being treated as bond order 1 +175: [20:24:14] non kekulizable aromatic bond being treated as bond order 1 +175: [20:24:14] non kekulizable aromatic bond being treated as bond order 1 +175: [20:24:14] non kekulizable aromatic bond being treated as bond order 1 +175: [20:24:14] non kekulizable aromatic bond being treated as bond order 1 +125: Warning: Atom Count for residue ASN157A does not match expected count +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 +161: file rxn_test3_1.png gave hash 786828249U not the expected 4189980366U +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +69: check isomorphism +141: [20:24:14] Rep: 60 Mol:0 +141: [20:24:14] Rep: 60 Mol:4 +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +141: [20:24:14] Rep: 80 Mol:3 +141: [20:24:14] Rep: 80 Mol:7 +141: [20:24:14] Rep: 80 Mol:11 +141: [20:24:14] Rep: 60 Mol:8 +141: [20:24:14] Rep: 80 Mol:15 +141: [20:24:14] Rep: 80 Mol:19 +161: Done +161: ----------------- Test 4: some examples from SMARTS in testing +161: draw! +141: [20:24:14] Rep: 80 Mol:23 +141: [20:24:14] Rep: 80 Mol:27 +141: [20:24:14] Rep: 80 Mol:31 +141: [20:24:14] Rep: 60 Mol:12 +141: [20:24:14] Rep: 60 Mol:16 +141: [20:24:14] Rep: 60 Mol:20 +141: [20:24:14] Rep: 60 Mol:24 +141: [20:24:14] Rep: 60 Mol:28 +148: [20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +141: [20:24:14] Rep: 40 Mol:2 +141: [20:24:14] Rep: 40 Mol:6 +141: [20:24:14] Rep: 40 Mol:10 +141: [20:24:14] Rep: 40 Mol:14 +141: [20:24:14] Rep: 40 Mol:18 +141: [20:24:14] Rep: 40 Mol:22 +141: [20:24:14] Rep: 40 Mol:26 +160: [20:24:14] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [20:24:14] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +141: [20:24:14] Rep: 40 Mol:30 +160: file testHandDrawn-1.svg gave hash 2072486955U not the expected 2253418236U +160: [20:24:14] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [20:24:14] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +117: =>start test 2 WHIM custom +117: [20:24:14] test on : 365 molecules done +148: .[20:24:14] Molecule does not have explicit Hs. Consider calling AddHs() +162: ...................... +162: ---------------------------------------------------------------------- +162: Ran 35 tests in 0.394s +162: +162: OK +162: json lasso +161: file rxn_test4_1.png gave hash 1704194173U not the expected 2745201873U +141: [20:24:14] Rep: 60 Mol:1 +141: [20:24:15] Rep: 60 Mol:5 +141: [20:24:15] Rep: 60 Mol:9 +141: [20:24:15] Rep: 60 Mol:13 +141: [20:24:15] Rep: 60 Mol:17 +141: [20:24:15] Rep: 60 Mol:21 +161: done +141: [20:24:15] Rep: 60 Mol:25 +141: [20:24:15] Rep: 60 Mol:29 +160: file testHandDrawn-1.png gave hash 70252907U not the expected 3894611804U +137/236 Test #162: pyMolDraw2D ............................ Passed 1.06 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: [00:24:58] Molecule does not have explicit Hs. Consider calling AddHs() -141: [00:24:58] Rep: 20 Mol:25 -141: [00:24:58] Rep: 20 Mol:29 -161: file rxn_test1_7.png gave hash 1360101162U not the expected 1461397406U -117: =>start test morse custom -161: file rxn_test1_7.svg gave hash 2324077060U not the expected 1831465890U +160: [20:24:15] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [20:24:15] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +98: . +98: ---------------------------------------------------------------------- +98: Ran 11 tests in 1.833s +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 0.07329678535461426 seconds +98: Skipped 10000000 in 0.8143579959869385 seconds +98: Skipped 10000000 in 0.650404691696167 seconds +161: file rxn_test4_2.png gave hash 30753303U not the expected 3094925886U +40: [20:24:15] done: 500000 +40: [20:24:15] Done +160: file testHandDrawn-2.svg gave hash 1534109833U not the expected 794717511U +160: [20:24:15] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [20:24:15] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +176: .... +176: ---------------------------------------------------------------------- +176: Ran 4 tests in 0.018s +176: +176: OK +175: [20:24:15] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +175: [20:24:15] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 161: Done -161: ----------------- Test 2: some examples that caused problems in testing -117: [00:24:58] test on : 365 molecules done -141: [00:24:58] Rep: 20 Mol:3 -148: [00:24:58] Molecule does not have explicit Hs. Consider calling AddHs() -141: [00:24:58] Rep: 20 Mol:7 -141: [00:24:58] Rep: 20 Mol:11 -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: -136/236 Test #68: testMrvToMol ........................... Passed 1.86 sec +138/236 Test #161: moldraw2DRxnTest1 ...................... Passed 1.18 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 -141: [00:24:58] Rep: 20 Mol:15 -141: [00:24:58] Rep: 20 Mol:19 -141: [00:24:58] Rep: 20 Mol:23 -141: [00:24:58] Rep: 20 Mol:27 -141: [00:24:58] Rep: 20 Mol:31 -148: [00:24:58] Molecule does not have explicit Hs. Consider calling AddHs() -126: Warning: Atom Count for residue LYS80A does not match expected count -148: [00:24:58] Molecule does not have explicit Hs. Consider calling AddHs() -161: file rxn_test2_1.png gave hash 3339775168U not the expected 3551633840U -141: [00:24:58] Rep: 20 Mol:0 -141: [00:24:58] Rep: 20 Mol:4 -141: [00:24:58] Rep: 20 Mol:8 -167: .... -167: ---------------------------------------------------------------------- -167: Ran 4 tests in 0.027s -167: -167: OK -141: [00:24:58] Rep: 20 Mol:12 -141: [00:24:58] Rep: 20 Mol:16 -160: file testPNGMetadata_2.png gave hash 2637596984U not the expected 1797853056U -148: [00:24:58] Molecule does not have explicit Hs. Consider calling AddHs() -141: [00:24:58] Rep: 20 Mol:20 -141: [00:24:58] Rep: 20 Mol:24 -141: [00:24:58] Rep: 20 Mol:28 -162: ...................... -162: ---------------------------------------------------------------------- -162: Ran 35 tests in 0.330s -162: -162: OK -162: json lasso -175: [00:24:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -175: [00:24:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -148: [00:24:58] Molecule does not have explicit Hs. Consider calling AddHs() -40: [00:24:58] done: 500000 -40: [00:24:58] Done -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 -137/236 Test #167: pyMolHash .............................. Passed 0.40 sec +143: [20:24:15] Rep: 100 Mol:3 +143: [20:24:15] Rep: 100 Mol:7 +143: [20:24:15] Rep: 100 Mol:11 +143: [20:24:15] Rep: 100 Mol:15 +143: [20:24:15] Rep: 100 Mol:19 +143: [20:24:15] Rep: 100 Mol:23 +143: [20:24:15] Rep: 100 Mol:27 +143: [20:24:15] Rep: 100 Mol:31 +160: file testHandDrawn-2.png gave hash 4273438430U not the expected 1443443188U +139/236 Test #98: pyChemReactionEnumerations ............. Passed 2.24 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 -178: Randomness seeded to: 1074423345 -178: =============================================================================== -178: All tests passed (111 assertions in 3 test cases) -178: -148: [00:24:58] Molecule does not have explicit Hs. Consider calling AddHs() -138/236 Test #178: deprotectTest .......................... Passed 0.10 sec +89: [20:24:15] Explicit valence for atom # 9 N, 5, is greater than permitted +143: [20:24:15] Rep: 100 Mol:2 +143: [20:24:15] Rep: 100 Mol:6 +143: [20:24:15] Rep: 100 Mol:10 +143: [20:24:15] Rep: 100 Mol:14 +143: [20:24:15] Rep: 100 Mol:18 +160: [20:24:15] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [20:24:15] 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: [20:24:15] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [20:24:15] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +40: [20:24:15] Testing hanoi with a functor. +141: [20:24:15] Rep: 80 Mol:0 +141: [20:24:15] Rep: 80 Mol:4 +141: [20:24:15] Rep: 80 Mol:8 +141: [20:24:15] Rep: 80 Mol:12 +141: [20:24:15] Rep: 80 Mol:16 +141: [20:24:15] Rep: 80 Mol:20 +141: [20:24:15] Rep: 80 Mol:24 +141: [20:24:15] Rep: 80 Mol:28 +140/236 Test #176: pyCIPLabelsWrapTest .................... Passed 0.38 sec +143: [20:24:15] Rep: 100 Mol:22 +143: [20:24:15] Rep: 100 Mol:26 +141: [20:24:15] Rep: 80 Mol:1 +151: 1251356385 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 -161: file rxn_test2_2_1.png gave hash 457778262U not the expected 1268122583U -159: processing -159: launch :0 -159: launch :1 -159: launch :2 -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 :3 -175: =============================================================================== -175: All tests passed (6577 assertions in 19 test cases) -175: -139/236 Test #175: testCIPLabeler ......................... Passed 0.36 sec +143: [20:24:15] Rep: 100 Mol:30 +141: [20:24:15] Rep: 80 Mol:5 +141: [20:24:15] Rep: 80 Mol:9 +141: [20:24:15] Rep: 80 Mol:13 +141: [20:24:15] Rep: 80 Mol:17 +141: [20:24:15] Rep: 80 Mol:21 +141: [20:24:15] Rep: 80 Mol:25 +141: [20:24:15] Rep: 80 Mol:29 +172: ..........[20:24:15] Too many matching bond pairs (1032) so can't continue. +40: [20:24:15] Done +40: [20:24:15] Testing basic partition refinement. +40: [20:24:15] Done +40: [20:24:15] Testing partition refinement with neighbors. +40: [20:24:15] Done +40: [20:24:15] testing canonicalization via tie breaking. +40: [20:24:15] Done +40: [20:24:15] testing canonicalization using the wrapper. +122: =>start test GETAWAY +122: [20:24:15] test on : 365 molecules done +141/236 Test #122: testGETAWAY ............................ Passed 2.01 sec +160: file testHandDrawn-3.png gave hash 258221924U not the expected 865629432U 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 -148: [00:24:58] Molecule does not have explicit Hs. Consider calling AddHs() -161: file rxn_test2_2_2.png gave hash 4285088210U not the expected 82821108U -40: [00:24:58] Testing hanoi with a functor. -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: .[00:24:58] Molecule does not have explicit Hs. Consider calling AddHs() -40: [00:24:58] Done -40: [00:24:58] Testing basic partition refinement. -40: [00:24:58] Done -40: [00:24:58] Testing partition refinement with neighbors. -40: [00:24:58] Done -40: [00:24:58] testing canonicalization via tie breaking. -40: [00:24:58] Done -40: [00:24:58] testing canonicalization using the wrapper. -161: file rxn_test2_2_3.png gave hash 660865433U not the expected 3828365604U +160: [20:24:15] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [20:24:15] 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 +160: [20:24:15] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [20:24:15] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +147: [20:24:15] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +40: [20:24:15] Done +40: [20:24:15] testing some specific ordering problems +40: [20:24:15] Finished +40: [20:24:15] testing chiral invariants. +40: [20:24:15] Finished +40: [20:24:15] testing unique ranks in w.r.t. renumbering. 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, 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0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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, ] 180: -40: [00:24:58] Done -40: [00:24:58] testing some specific ordering problems -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 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, 0.6, 1, 0.3, 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, 1.3, 1.3, 0.6, 1, 0.6, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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, ] 180: -40: [00:24:58] Finished -40: [00:24:58] testing chiral invariants. -40: [00:24:58] Finished -40: [00:24:58] testing unique ranks in w.r.t. renumbering. 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, 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0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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, 0.3, 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: -140/236 Test #180: testReducedGraphs ...................... Passed 0.09 sec +142/236 Test #175: testCIPLabeler ......................... Passed 0.48 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 -161: file rxn_test2_2_4.png gave hash 1904681261U not the expected 1230108677U -141/236 Test #162: pyMolDraw2D ............................ Passed 0.85 sec +141: [20:24:15] Rep: 60 Mol:2 +143/236 Test #180: testReducedGraphs ...................... Passed 0.07 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 -161: Done -161: ----------------- Test 3: test reactant highlighting -160: [00:24:58] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [00:24:58] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. -176: .... -176: ---------------------------------------------------------------------- -176: Ran 4 tests in 0.045s -176: -176: OK -141: [00:24:58] Rep: 40 Mol:3 -141: [00:24:58] Rep: 40 Mol:7 -141: [00:24:58] Rep: 40 Mol:11 -141: [00:24:58] Rep: 40 Mol:15 -141: [00:24:58] Rep: 40 Mol:19 -160: file testHandDrawn-1.svg gave hash 2072486955U not the expected 2253418236U -160: [00:24:58] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [00:24:58] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. -141: [00:24:58] Rep: 40 Mol:1 -141: [00:24:58] Rep: 40 Mol:5 -141: [00:24:58] Rep: 40 Mol:9 -141: [00:24:58] Rep: 40 Mol:23 -183: [00:24:58] ------------------------------------- -183: [00:24:58] Test1 -141: [00:24:58] Rep: 40 Mol:13 -141: [00:24:58] Rep: 40 Mol:17 -141: [00:24:58] Rep: 40 Mol:21 -141: [00:24:58] Rep: 40 Mol:25 -141: [00:24:58] Rep: 40 Mol:27 -141: [00:24:58] Rep: 40 Mol:31 -141: [00:24:58] Rep: 40 Mol:29 -161: file rxn_test3_1.png gave hash 786828249U not the expected 4189980366U -142/236 Test #176: pyCIPLabelsWrapTest .................... Passed 0.46 sec +148: [20:24:15] Molecule does not have explicit Hs. Consider calling AddHs() +117: =>start test 1 WHIM custom +117: [20:24:15] test on : 365 molecules done +141: [20:24:15] Rep: 60 Mol:6 +141: [20:24:15] Rep: 60 Mol:10 +141: [20:24:15] Rep: 60 Mol:14 +141: [20:24:15] Rep: 60 Mol:18 +141: [20:24:15] Rep: 60 Mol:22 +141: [20:24:15] Rep: 60 Mol:26 +141: [20:24:15] Rep: 60 Mol:30 +160: file testHandDrawn-4.png gave hash 2602629668U not the expected 3919767093U +178: Randomness seeded to: 1411176621 +178: =============================================================================== +178: All tests passed (111 assertions in 3 test cases) +178: +144/236 Test #178: deprotectTest .......................... Passed 0.13 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 -40: [00:24:58] Finished -40: [00:24:58] testing mol fragments. -40: [00:24:58] Finished -40: [00:24:58] testing protein round-tripping. -161: Done -161: ----------------- Test 4: some examples from SMARTS in testing -161: draw! -148: [00:24:58] Molecule does not have explicit Hs. Consider calling AddHs() -160: file testHandDrawn-1.png gave hash 70252907U not the expected 3894611804U -141: [00:24:58] Rep: 40 Mol:0 -141: [00:24:58] Rep: 40 Mol:4 -141: [00:24:58] Rep: 40 Mol:8 -141: [00:24:58] Rep: 40 Mol:12 -141: [00:24:58] Rep: 40 Mol:16 -141: [00:24:58] Rep: 20 Mol:2 -141: [00:24:58] Rep: 40 Mol:20 -141: [00:24:58] Rep: 20 Mol:6 -141: [00:24:58] Rep: 20 Mol:10 -141: [00:24:58] Rep: 40 Mol:24 -141: [00:24:58] Rep: 40 Mol:28 -141: [00:24:58] Rep: 20 Mol:14 -141: [00:24:58] Rep: 20 Mol:18 -141: [00:24:58] Rep: 20 Mol:22 -141: [00:24:58] Rep: 20 Mol:26 -141: [00:24:58] Rep: 20 Mol:30 -161: file rxn_test4_1.png gave hash 1704194173U not the expected 2745201873U -98: . -98: ---------------------------------------------------------------------- -98: Ran 11 tests in 1.830s -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 0.0688173770904541 seconds -98: Skipped 10000000 in 0.7095990180969238 seconds -98: Skipped 10000000 in 0.7519397735595703 seconds -161: done -147: [00:24:58] UFFTYPER: Warning: hybridization set to SP3 for atom 6 -160: [00:24:58] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [00:24:58] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. -160: file testHandDrawn-2.svg gave hash 1534109833U not the expected 794717511U -160: [00:24:58] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [00:24:58] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. -172: ..........[00:24:58] Too many matching bond pairs (1032) so can't continue. -125: Warning: Atom Count for residue GLU150A does not match expected count -143/236 Test #98: pyChemReactionEnumerations ............. Passed 2.27 sec -141: [00:24:58] Rep: 60 Mol:3 +147: [20:24:15] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +40: [20:24:15] Finished +40: [20:24:15] testing mol fragments. +40: [20:24:15] Finished +40: [20:24:15] testing protein round-tripping. +143: [20:24:15] Rep: 100 Mol:1 +143: [20:24:15] Rep: 100 Mol:5 +143: [20:24:15] Rep: 100 Mol:9 +143: [20:24:15] Rep: 100 Mol:13 +143: [20:24:15] Rep: 100 Mol:17 +143: [20:24:15] Rep: 100 Mol:21 +143: [20:24:15] Rep: 100 Mol:25 +143: [20:24:15] Rep: 100 Mol:29 +126: Warning: Atom Count for residue GLU150A does not match expected count +89: [20:24:15] Explicit valence for atom # 3 Al, 6, is greater than permitted +183: [20:24:15] ------------------------------------- +183: [20:24:15] Test1 +147: [20:24:15] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +126: Warning: Atom Count for residue ASN157A does not match expected count +89: [20:24:15] Explicit valence for atom # 4 Al, 6, is greater than permitted +89: [20:24:15] Explicit valence for atom # 10 Si, 6, is greater than permitted +147: [20:24:15] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +147: [20:24:15] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +148: [20:24:15] Molecule does not have explicit Hs. Consider calling AddHs() +147: [20:24:15] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +145/236 Test #182: trajectoryTest ......................... Passed 0.30 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 -141: [00:24:58] Rep: 60 Mol:7 -141: [00:24:58] Rep: 60 Mol:11 -141: [00:24:58] Rep: 60 Mol:15 -141: [00:24:58] Rep: 60 Mol:19 -141: [00:24:58] Rep: 60 Mol:23 -141: [00:24:58] Rep: 60 Mol:27 -141: [00:24:58] Rep: 60 Mol:31 -143: [00:24:58] Rep: 100 Mol:3 -143: [00:24:58] Rep: 100 Mol:7 -143: [00:24:58] Rep: 100 Mol:11 -143: [00:24:58] Rep: 100 Mol:15 -143: [00:24:58] Rep: 100 Mol:19 -143: [00:24:58] Rep: 100 Mol:23 -143: [00:24:58] Rep: 100 Mol:27 -143: [00:24:58] Rep: 100 Mol:31 -160: file testHandDrawn-2.png gave hash 4273438430U not the expected 1443443188U -147: [00:24:58] UFFTYPER: Warning: hybridization set to SP3 for atom 6 -125: Warning: Atom Count for residue ASN157A does not match expected count -161: file rxn_test4_2.png gave hash 30753303U not the expected 3094925886U -160: [00:24:58] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [00:24:58] 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: [00:24:58] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [00:24:58] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. -141: [00:24:59] Rep: 60 Mol:1 -141: [00:24:59] Rep: 60 Mol:5 -141: [00:24:59] Rep: 60 Mol:9 -141: [00:24:59] Rep: 60 Mol:13 -141: [00:24:59] Rep: 60 Mol:17 -141: [00:24:59] Rep: 60 Mol:21 -141: [00:24:59] Rep: 60 Mol:25 -141: [00:24:59] Rep: 60 Mol:29 +143: [20:24:15] Rep: 100 Mol:0 +143: [20:24:15] Rep: 100 Mol:4 +143: [20:24:15] Rep: 100 Mol:8 +143: [20:24:15] Rep: 100 Mol:12 +143: [20:24:15] Rep: 100 Mol:16 +143: [20:24:15] Rep: 100 Mol:20 +143: [20:24:15] Rep: 100 Mol:24 +143: [20:24:15] Rep: 100 Mol:28 179: ..... 179: ---------------------------------------------------------------------- -179: Ran 5 tests in 0.046s +179: Ran 5 tests in 0.045s 179: 179: OK 179: Testing tert-butyldimethylsilyl @@ -29451,277 +29578,489 @@ 179: Testing acetamide 179: Testing carbobenzyloxy 179: Testing Acetal/Ketal -160: file testHandDrawn-3.png gave hash 258221924U not the expected 865629432U -161: Done -144/236 Test #161: moldraw2DRxnTest1 ...................... Passed 1.28 sec +89: [20:24:15] Explicit valence for atom # 2 O, 4, is greater than permitted +146/236 Test #179: pyDeprotect ............................ Passed 0.57 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 -160: [00:24:59] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [00:24:59] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. -145/236 Test #182: trajectoryTest ......................... Passed 0.45 sec -147: [00:24:59] UFFTYPER: Warning: hybridization set to SP3 for atom 6 -147: [00:24:59] UFFTYPER: Warning: hybridization set to SP3 for atom 11 -147: [00:24:59] UFFTYPER: Warning: hybridization set to SP3 for atom 11 -147: [00:24:59] UFFTYPER: Warning: hybridization set to SP3 for atom 11 -148: [00:24:59] Molecule does not have explicit Hs. Consider calling AddHs() -141: [00:24:59] Rep: 60 Mol:0 -141: [00:24:59] Rep: 60 Mol:4 -141: [00:24:59] Rep: 60 Mol:8 -141: [00:24:59] Rep: 60 Mol:12 -141: [00:24:59] Rep: 60 Mol:16 -141: [00:24:59] Rep: 60 Mol:20 -141: [00:24:59] Rep: 60 Mol:24 -141: [00:24:59] Rep: 60 Mol:28 -141: [00:24:59] Rep: 40 Mol:2 -141: [00:24:59] Rep: 40 Mol:6 -141: [00:24:59] Rep: 40 Mol:10 +89: [20:24:15] Explicit valence for atom # 3 Al, 6, is greater than permitted +89: [20:24:15] Explicit valence for atom # 3 Be, 4, is greater than permitted +141: [20:24:15] Rep: 80 Mol:2 +141: [20:24:15] Rep: 80 Mol:6 +141: [20:24:15] Rep: 80 Mol:10 +141: [20:24:15] Rep: 80 Mol:14 +141: [20:24:15] Rep: 80 Mol:18 +141: [20:24:15] Rep: 80 Mol:22 +141: [20:24:15] Rep: 80 Mol:26 +141: [20:24:15] Rep: 80 Mol:30 +89: [20:24:15] Explicit valence for atom # 27 P, 6, is greater than permitted +89: =============================================================================== +89: All tests passed (21562 assertions in 3 test cases) +89: +147/236 Test #89: multithreadedSupplierCatchTest ......... Passed 2.99 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 -146/236 Test #179: pyDeprotect ............................ Passed 0.71 sec -141: [00:24:59] Rep: 40 Mol:14 -141: [00:24:59] Rep: 40 Mol:18 +181: ..... +181: ---------------------------------------------------------------------- +181: Ran 5 tests in 0.042s +181: +181: OK +187: [20:24:15] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [20:24:15] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [20:24:15] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [20:24:15] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [20:24:15] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [20:24:15] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [20:24:15] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [20:24:15] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [20:24:15] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [20:24:15] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [20:24:15] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [20:24:15] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [20:24:15] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [20:24:15] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [20:24:15] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [20:24:15] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [20:24:15] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [20:24:15] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [20:24:15] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [20:24:15] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [20:24:15] WARNING: not removing hydrogen atom with dummy atom neighbors +148/236 Test #187: testRGroupDecompInternals .............. Passed 0.04 sec +40: [20:24:15] Finished +40: [20:24:15] testing stability w.r.t. renumbering. +148: [20:24:15] Molecule does not have explicit Hs. Consider calling AddHs() 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 -160: file testHandDrawn-4.svg gave hash 1880974760U not the expected 2146113517U -160: [00:24:59] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [00:24:59] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. -141: [00:24:59] Rep: 40 Mol:22 -141: [00:24:59] Rep: 40 Mol:26 -141: [00:24:59] Rep: 40 Mol:30 -184: Randomness seeded to: 3550881767 -184: =============================================================================== -184: All tests passed (171 assertions in 5 test cases) -184: -147/236 Test #184: substructLibraryCatchTest .............. Passed 0.49 sec +149/236 Test #181: pyReducedGraphs ........................ Passed 0.74 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 -160: file testHandDrawn-4.png gave hash 2602629668U not the expected 3919767093U -181: ..... -181: ---------------------------------------------------------------------- -181: Ran 5 tests in 0.045s -181: -181: OK -143: [00:24:59] Rep: 100 Mol:0 -143: [00:24:59] Rep: 100 Mol:4 -143: [00:24:59] Rep: 100 Mol:8 -143: [00:24:59] Rep: 100 Mol:12 -143: [00:24:59] Rep: 100 Mol:16 -143: [00:24:59] Rep: 100 Mol:20 -143: [00:24:59] Rep: 100 Mol:24 -143: [00:24:59] Rep: 100 Mol:28 -141: [00:24:59] Rep: 80 Mol:3 -141: [00:24:59] Rep: 80 Mol:7 -141: [00:24:59] Rep: 80 Mol:11 -141: [00:24:59] Rep: 80 Mol:15 -141: [00:24:59] Rep: 80 Mol:19 -141: [00:24:59] Rep: 80 Mol:23 -141: [00:24:59] Rep: 80 Mol:27 -141: [00:24:59] Rep: 80 Mol:31 -187: [00:24:59] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [00:24:59] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [00:24:59] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [00:24:59] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [00:24:59] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [00:24:59] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [00:24:59] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [00:24:59] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [00:24:59] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [00:24:59] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [00:24:59] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [00:24:59] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [00:24:59] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [00:24:59] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [00:24:59] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [00:24:59] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [00:24:59] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [00:24:59] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [00:24:59] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [00:24:59] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [00:24:59] WARNING: not removing hydrogen atom with dummy atom neighbors -148/236 Test #187: testRGroupDecompInternals .............. Passed 0.12 sec +183: [20:24:16] done +40: [20:24:16] Finished +40: [20:24:16] testing smiles round-tripping. +183: [20:24:16] ------------------------------------- +183: [20:24:16] Test2 +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 0.111 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 0.012 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 0.015 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 0.118 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 0.092 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 0.114 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 0.113 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 0.015 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 0.015 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 0.373 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 0.471 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 0.437 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 +163: Time elapsed 0.009 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 +151: 899965594 +151: =============================================================================== +151: All tests passed (73 assertions in 3 test cases) +151: +150/236 Test #151: molAlignCatchTest ...................... Passed 2.41 sec +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 0.091 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 0.026 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 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 -183: [00:24:59] done -190: [00:24:59] test1: basics -183: [00:24:59] ------------------------------------- -183: [00:24:59] Test2 -143: [00:24:59] Rep: 100 Mol:1 -143: [00:24:59] Rep: 100 Mol:5 -143: [00:24:59] Rep: 100 Mol:9 -143: [00:24:59] Rep: 100 Mol:13 -143: [00:24:59] Rep: 100 Mol:17 -143: [00:24:59] Rep: 100 Mol:21 -143: [00:24:59] Rep: 100 Mol:25 -143: [00:24:59] Rep: 100 Mol:29 -190: [00:24:59] done -190: [00:24:59] test2: basic writing +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 +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 +186: [20:24:16] Non terminal R group defined. To allow set allowNonTerminalRGroups in RGroupDecompositionParameters +186: [20:24:16] WARNING: not removing hydrogen atom with dummy atom neighbors +190: [20:24:16] test1: basics +141: [20:24:16] done +141: [20:24:16] ------------------------------------- +141: [20:24:16] Test MMFF multithreading2 +190: [20:24:16] done +190: [20:24:16] 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: [00:24:59] done -190: [00:24:59] test3: writing conformers +190: [20:24:16] done +190: [20:24:16] 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: [00:24:59] done -190: [00:24:59] test4: writing properties +190: [20:24:16] done +190: [20:24:16] 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: [00:24:59] done -190: [00:24:59] test5: writing partial charges +190: [20:24:16] done +190: [20:24:16] 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: [00:24:59] testing parse options -190: [00:24:59] done -190: [00:24:59] testing github #2046: CIPRank values from JSONDataToMols are not unsigned +190: [20:24:16] testing parse options +190: [20:24:16] done +190: [20:24:16] 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: [00:24:59] done -190: [00:24:59] testing 'either' stereochemistry -190: [00:24:59] done -149/236 Test #190: molInterchangeTest1 .................... Passed 0.07 sec -148: [00:24:59] Molecule does not have explicit Hs. Consider calling AddHs() -126: Warning: Atom Count for residue GLU150A does not match expected count -117: =>start test AUTOCORR3D custom -117: [00:24:59] test on : 365 molecules done -141: [00:24:59] Rep: 80 Mol:1 -141: [00:24:59] Rep: 80 Mol:5 -141: [00:24:59] Rep: 80 Mol:9 -141: [00:24:59] Rep: 80 Mol:13 -141: [00:24:59] Rep: 80 Mol:17 +190: [20:24:16] done +190: [20:24:16] testing 'either' stereochemistry +190: [20:24:16] 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 -150/236 Test #181: pyReducedGraphs ........................ Passed 0.93 sec +188: Randomness seeded to: 4186881934 +188: =============================================================================== +188: All tests passed (1475 assertions in 14 test cases) +188: +152/236 Test #188: rgroupCatchTests ....................... Passed 0.39 sec +69: [20:24:16] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +69: [20:24:16] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +69: [20:24:16] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +69: [20:24:16] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored 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 -146: [00:24:57] --------------------------------- -146: [00:24:57] test3 +69: [20:24:16] deprecated group abbreviation ignored on line 24 +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: [20:24:16] +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# 0x00007FED9A6C8531 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 4# 0x00007FED9A6D1DFA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 5# 0x00007FED9A6D217D 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# 0x000055CD737E6C15 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 10# 0x000055CD7384D372 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 11# 0x000055CD737CD9A3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 12# 0x00007FED99C33CA8 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# 0x000055CD737CDAD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: ---------- +69: **** +69: +146: [20:24:13] --------------------------------- +146: [20:24:13] test3 146: -146: [00:24:57] --------------------------------- -146: [00:24:57] test4 +146: [20:24:13] --------------------------------- +146: [20:24:13] test4 146: -146: [00:24:57] --------------------------------- -146: [00:24:57] test5 +146: [20:24:13] --------------------------------- +146: [20:24:13] test5 146: -146: [00:24:59] --------------------------------- -146: [00:24:59] test6 +146: [20:24:16] --------------------------------- +146: [20:24:16] test6 146: -146: [00:24:59] --------------------------------- -146: [00:24:59] test15Dists +146: [20:24:16] --------------------------------- +146: [20:24:16] test15Dists 146: -146: [00:24:59] --------------------------------- -146: [00:24:59] test Issue 215 +146: [20:24:16] --------------------------------- +146: [20:24:16] test Issue 215 146: -146: [00:24:59] --------------------------------- -146: [00:24:59] testMultipleConfs +146: [20:24:16] --------------------------------- +146: [20:24:16] testMultipleConfs 146: -146: [00:24:59] --------------------------------- -146: [00:24:59] testMultipleConfsExpTors +146: [20:24:16] --------------------------------- +146: [20:24:16] testMultipleConfsExpTors 146: -146: [00:24:59] --------------------------------- -146: [00:24:59] testIssue227 +146: [20:24:16] --------------------------------- +146: [20:24:16] testIssue227 146: -146: [00:24:59] --------------------------------- -146: [00:24:59] testIssue236 +146: [20:24:16] --------------------------------- +146: [20:24:16] testIssue236 146: -146: [00:24:59] --------------------------------- -146: [00:24:59] testOrdering +146: [20:24:16] --------------------------------- +146: [20:24:16] testOrdering 146: -146: [00:24:59] --------------------------------- -146: [00:24:59] testIssue244 +146: [20:24:16] --------------------------------- +146: [20:24:16] testIssue244 146: -146: [00:24:59] --------------------------------- -146: [00:24:59] testIssue251 +146: [20:24:16] --------------------------------- +146: [20:24:16] testIssue251 146: -146: [00:24:59] --------------------------------- -146: [00:24:59] testIssue276 -146: [00:24:59] --------------------------------- -146: [00:24:59] testIssue284 +146: [20:24:16] --------------------------------- +146: [20:24:16] testIssue276 +146: [20:24:16] --------------------------------- +146: [20:24:16] testIssue284 146: -146: [00:24:59] --------------------------------- -146: [00:24:59] testIssue285 +146: [20:24:16] --------------------------------- +146: [20:24:16] testIssue285 146: -146: [00:24:59] --------------------------------- -146: [00:24:59] testIssue355 +146: [20:24:16] --------------------------------- +146: [20:24:16] testIssue355 146: -146: [00:24:59] --------------------------------- -146: [00:24:59] testRandomCoords +146: [20:24:16] --------------------------------- +146: [20:24:16] testRandomCoords 146: -146: [00:24:59] --------------------------------- -146: [00:24:59] test sf.net issue 1989539 +146: [20:24:16] --------------------------------- +146: [20:24:16] test sf.net issue 1989539 146: -146: [00:24:59] --------------------------------- -146: [00:24:59] test sf.net issue 2091864 +146: [20:24:16] --------------------------------- +146: [20:24:16] test sf.net issue 2091864 146: -146: [00:24:59] --------------------------------- -146: [00:24:59] test constrained embedding +146: [20:24:16] --------------------------------- +146: [20:24:16] test constrained embedding 146: -146: [00:24:59] ssd: 0.0752641 -146: [00:24:59] ssd: 0.0659363 -141: [00:24:59] Rep: 80 Mol:21 -141: [00:24:59] Rep: 80 Mol:25 -141: [00:24:59] Rep: 80 Mol:29 -143: [00:24:59] Rep: 100 Mol:2 -143: [00:24:59] Rep: 100 Mol:6 -143: [00:24:59] Rep: 100 Mol:10 -143: [00:24:59] Rep: 100 Mol:14 -143: [00:24:59] Rep: 100 Mol:18 -143: [00:24:59] Rep: 100 Mol:22 -143: [00:24:59] Rep: 100 Mol:26 -143: [00:24:59] Rep: 100 Mol:30 -151/236 Test #42: resMolSupplierTest ..................... Passed 3.20 sec +146: [20:24:16] ssd: 0.0752641 +146: [20:24:16] ssd: 0.0659363 +173: Randomness seeded to: 3903386075 +173: [20:24:16] Writing the enumerated file may take quite some time and result in a large file. +191: Randomness seeded to: 2821014142 +191: [20:24:16] unrecognized bond type 12 set to zero while writing +191: [20:24:16] unrecognized bond type 0 set to zero while writing +191: =============================================================================== +191: All tests passed (125 assertions in 7 test cases) +191: +153/236 Test #191: molInterchangeCatchTest ................ Passed 0.09 sec +111: [20:24:16] done +111: [20:24:16] ------------------------------------- +111: [20:24:16] Test Issue252: Bad definitions for Crippen atom types. 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 -191: Randomness seeded to: 902914009 -191: [00:24:59] unrecognized bond type 12 set to zero while writing -191: [00:24:59] unrecognized bond type 0 set to zero while writing -141: [00:24:59] Rep: 80 Mol:0 -141: [00:24:59] Rep: 80 Mol:4 -141: [00:24:59] Rep: 80 Mol:8 -126: Warning: Atom Count for residue ASN157A does not match expected count -141: [00:24:59] Rep: 80 Mol:12 -141: [00:24:59] Rep: 80 Mol:16 -191: =============================================================================== -191: All tests passed (125 assertions in 7 test cases) -191: -141: [00:24:59] Rep: 80 Mol:20 -141: [00:24:59] Rep: 80 Mol:24 -152/236 Test #191: molInterchangeCatchTest ................ Passed 0.07 sec -141: [00:24:59] Rep: 80 Mol:28 -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 +111: [20:24:16] done +111: [20:24:16] ------------------------------------- +111: [20:24:16] Test calculation of ChiVs. +111: [20:24:16] done +111: [20:24:16] ------------------------------------- +111: [20:24:16] Test calculation of ChiNs. +111: [20:24:16] done +111: [20:24:16] ------------------------------------- +111: [20:24:16] Test calculation of HallKierAlpha. +111: [20:24:16] done +111: [20:24:16] ------------------------------------- +111: [20:24:16] Test calculation of Kappa1. +111: [20:24:16] done +111: [20:24:16] ------------------------------------- +111: [20:24:16] Test calculation of Kappa2. +111: [20:24:16] done +111: [20:24:16] ------------------------------------- +111: [20:24:16] Test calculation of Kappa3. +111: [20:24:16] done +111: [20:24:16] ------------------------------------- +111: [20:24:16] Test Crippen atom type calculations. +111: [20:24:16] done +111: [20:24:16] ------------------------------------- +111: [20:24:16] Test ring descriptors +111: [20:24:16] done +111: [20:24:16] ------------------------------------- +111: [20:24:16] Test other count descriptors. +111: [20:24:16] done +111: [20:24:16] ------------------------------------- +111: [20:24:16] Test MQN 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: @@ -29735,413 +30074,263 @@ 193: 2 0->3 order: 1 193: 3 0->4 order: 1 193: 4 0->5 order: 1 -193: [00:24:59] SLN Parse Error: syntax error while parsing: CH4[I=13] -193: [00:24:59] Failed parsing SLN 'CH4[I=13]' -193: [00:24:59] SLN Parser error: Atom ID 1 appears *after* its ring closure. -193: [00:24:59] SLN Parser error: Ring closure 1 does not have a corresponding opener. -193: [00:24:59] SLN Parse Error: syntax error while parsing: CH2(C@1H2)CH2(CH2CH2C[1]H2) -193: [00:24:59] Failed parsing SLN 'CH2(C@1H2)CH2(CH2CH2C[1]H2)' -193: [00:24:59] SLN Parse Error: syntax error while parsing: CH2(CH2[1])CH2(CH2CH2CH2@1) -193: [00:24:59] Failed parsing SLN 'CH2(CH2[1])CH2(CH2CH2CH2@1)' -193: [00:24:59] SLN Parse Error: syntax error while parsing: CH4 fff -193: [00:24:59] Failed parsing SLN 'CH4 fff' -193: [00:24:59] SLN Parse Error: syntax error while parsing: C[charge=+1] foo -193: [00:24:59] Failed parsing SLN 'C[charge=+1] foo' -193: [00:24:59] Query property 'is' ignored on non-query atom -193: [00:24:59] Query property 'is' ignored on non-query atom -153/236 Test #193: testSLNParse ........................... Passed 0.07 sec -141: [00:24:59] Rep: 60 Mol:2 +193: [20:24:16] SLN Parse Error: syntax error while parsing: CH4[I=13] +193: [20:24:16] Failed parsing SLN 'CH4[I=13]' +111: [20:24:16] done +111: [20:24:16] ------------------------------------- +111: [20:24:16] Test GitHub Issue 56. +111: [20:24:16] WARNING: not removing hydrogen atom without neighbors +111: [20:24:16] WARNING: not removing hydrogen atom without neighbors +111: [20:24:16] WARNING: not removing hydrogen atom without neighbors +111: [20:24:16] WARNING: not removing hydrogen atom without neighbors +111: [20:24:16] done +111: [20:24:16] ------------------------------------- +111: [20:24:16] Test Github92: Bad Crippen atom type for pyrrole H. +111: [20:24:16] done +111: [20:24:16] ------------------------------------- +111: [20:24:16] Test Github362: order dependence in Kier-Hall descriptors. +193: [20:24:16] SLN Parser error: Atom ID 1 appears *after* its ring closure. +193: [20:24:16] SLN Parser error: Ring closure 1 does not have a corresponding opener. +193: [20:24:16] SLN Parse Error: syntax error while parsing: CH2(C@1H2)CH2(CH2CH2C[1]H2) +193: [20:24:16] Failed parsing SLN 'CH2(C@1H2)CH2(CH2CH2C[1]H2)' +193: [20:24:16] SLN Parse Error: syntax error while parsing: CH2(CH2[1])CH2(CH2CH2CH2@1) +193: [20:24:16] Failed parsing SLN 'CH2(CH2[1])CH2(CH2CH2CH2@1)' +193: [20:24:16] SLN Parse Error: syntax error while parsing: CH4 fff +193: [20:24:16] Failed parsing SLN 'CH4 fff' +193: [20:24:16] SLN Parse Error: syntax error while parsing: C[charge=+1] foo +193: [20:24:16] Failed parsing SLN 'C[charge=+1] foo' +193: [20:24:16] Query property 'is' ignored on non-query atom +193: [20:24:16] Query property 'is' ignored on non-query atom +111: [20:24:16] done +111: [20:24:16] ------------------------------------- +111: [20:24:16] Test calculation of spiro and bridgehead counts. +111: [20:24:16] done +111: [20:24:16] ------------------------------------- +111: [20:24:16] Test Github694: ExactMolWt ignoring the mass of the electron +111: [20:24:16] done +111: [20:24:16] ------------------------------------- +111: [20:24:16] Testing Properties and KitchenSink +154/236 Test #193: testSLNParse ........................... Passed 0.07 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 +111: [20:24:16] ---Caught keyerror (bad property name)--- +111: [20:24:16] ------------------------------------- +111: [20:24:16] Test USR Descriptor +111: [20:24:16] done +111: [20:24:16] ------------------------------------- +111: [20:24:16] Test Github #1702: AUTOCORR2D.h not installed unless RDK_BUILD_DESCRIPTORS3D but is required +111: [20:24:16] done +111: [20:24:16] ------------------------------------- +111: [20:24:16] Test Github #1973: support P and S terms for TPSA calculation +111: [20:24:16] done +111: [20:24:16] ------------------------------------- +111: [20:24:16] Test Github #2948: Empty molecule has non-zero LabuteASA +111: [20:24:16] done +148: [20:24:16] Molecule does not have explicit Hs. Consider calling AddHs() +155/236 Test #111: testDescriptors ........................ Passed 3.44 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 -141: [00:24:59] Rep: 60 Mol:6 -141: [00:24:59] Rep: 60 Mol:10 -141: [00:24:59] Rep: 60 Mol:14 -141: [00:24:59] Rep: 60 Mol:18 -141: [00:24:59] Rep: 60 Mol:22 -141: [00:24:59] Rep: 60 Mol:26 -141: [00:24:59] Rep: 60 Mol:30 -111: [00:24:59] done -111: [00:24:59] ------------------------------------- -111: [00:24:59] Test Issue252: Bad definitions for Crippen atom types. -111: [00:24:59] done -111: [00:24:59] ------------------------------------- -111: [00:24:59] Test calculation of ChiVs. -111: [00:24:59] done -111: [00:24:59] ------------------------------------- -111: [00:24:59] Test calculation of ChiNs. -111: [00:24:59] done -111: [00:24:59] ------------------------------------- -111: [00:24:59] Test calculation of HallKierAlpha. -111: [00:24:59] done -111: [00:24:59] ------------------------------------- -111: [00:24:59] Test calculation of Kappa1. -111: [00:24:59] done -111: [00:24:59] ------------------------------------- -111: [00:24:59] Test calculation of Kappa2. -111: [00:24:59] done -111: [00:24:59] ------------------------------------- -111: [00:24:59] Test calculation of Kappa3. -111: [00:24:59] done -111: [00:24:59] ------------------------------------- -111: [00:24:59] Test Crippen atom type calculations. -111: [00:24:59] done -111: [00:24:59] ------------------------------------- -111: [00:24:59] Test ring descriptors -111: [00:24:59] done -111: [00:24:59] ------------------------------------- -111: [00:24:59] Test other count descriptors. -111: [00:24:59] done -111: [00:24:59] ------------------------------------- -111: [00:24:59] Test MQN -111: [00:24:59] done -111: [00:24:59] ------------------------------------- -111: [00:24:59] Test GitHub Issue 56. -111: [00:24:59] WARNING: not removing hydrogen atom without neighbors -111: [00:24:59] WARNING: not removing hydrogen atom without neighbors -111: [00:24:59] WARNING: not removing hydrogen atom without neighbors -111: [00:24:59] WARNING: not removing hydrogen atom without neighbors -111: [00:24:59] done -111: [00:24:59] ------------------------------------- -111: [00:24:59] Test Github92: Bad Crippen atom type for pyrrole H. -111: [00:24:59] done -111: [00:24:59] ------------------------------------- -111: [00:24:59] Test Github362: order dependence in Kier-Hall descriptors. -111: [00:24:59] done -111: [00:24:59] ------------------------------------- -111: [00:24:59] Test calculation of spiro and bridgehead counts. -111: [00:24:59] done -111: [00:24:59] ------------------------------------- -111: [00:24:59] Test Github694: ExactMolWt ignoring the mass of the electron -111: [00:24:59] done -111: [00:24:59] ------------------------------------- -111: [00:24:59] Testing Properties and KitchenSink -111: [00:24:59] ---Caught keyerror (bad property name)--- -111: [00:24:59] ------------------------------------- -111: [00:24:59] Test USR Descriptor -111: [00:24:59] done -111: [00:24:59] ------------------------------------- -111: [00:24:59] Test Github #1702: AUTOCORR2D.h not installed unless RDK_BUILD_DESCRIPTORS3D but is required -111: [00:24:59] done -111: [00:24:59] ------------------------------------- -111: [00:24:59] Test Github #1973: support P and S terms for TPSA calculation -111: [00:24:59] done -111: [00:24:59] ------------------------------------- -111: [00:24:59] Test Github #2948: Empty molecule has non-zero LabuteASA -111: [00:24:59] done -154/236 Test #111: testDescriptors ........................ Passed 2.88 sec +69: [20:24:16] 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: [20:24:16] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +40: [20:24:16] Finished +40: [20:24:16] testing github #1567: Non-canonical result from MolFragmentToSmiles() +40: [20:24:16] Finished +156/236 Test #40: hanoiTest .............................. Passed 3.92 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 -146: [00:24:59] --------------------------------- -146: [00:24:59] test sf.net issue 2091974 -146: -146: [00:24:59] --------------------------------- -146: [00:24:59] test sf.net issue 2835784 -146: -146: [00:24:59] --------------------------------- -146: [00:24:59] test sf.net issue 3019283 -146: -146: [00:24:59] --------------------------------- -146: [00:24:59] test sf.net issue 3238580 -146: -146: [00:24:59] --------------------------------- -146: [00:24:59] test sf.net issue 3483968 -146: -146: [00:24:59] --------------------------------- -146: [00:24:59] test github issue 55 -146: -146: [00:24:59] --------------------------------- -146: [00:24:59] test1 -146: -146: [00:24:59] --------------------------------- -146: [00:24:59] test multi-threading -146: -146: building molecules -40: [00:24:59] Finished -40: [00:24:59] testing stability w.r.t. renumbering. -146: generating reference data -186: [00:24:59] Non terminal R group defined. To allow set allowNonTerminalRGroups in RGroupDecompositionParameters -186: [00:24:59] WARNING: not removing hydrogen atom with dummy atom neighbors -151: 2061915990 -40: [00:24:59] Finished -40: [00:24:59] testing smiles round-tripping. -69: [00:24:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -69: [00:24:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -69: [00:24:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -69: [00:24:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -69: [00:24:59] deprecated group abbreviation ignored on line 24 -29: Checking against /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -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: [00:24:59] +69: ---------------------------------- +69: ---------------------------------- +69: [20:24:16] 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: 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::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# 0x00007F4415CC8531 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 4# 0x00007F4415CD1DFA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 5# 0x00007F4415CD217D 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# 0x0000563C49678C15 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 10# 0x0000563C496DF372 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 11# 0x0000563C4965F9A3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 12# 0x00007F4415233CA8 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# 0x0000563C4965FAD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +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# 0x000055CD737F3FFF in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 4# 0x000055CD7384D3EA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 5# 0x000055CD737CD9A3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 6# 0x00007FED99C33CA8 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# 0x000055CD737CDAD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 69: ---------- 69: **** 69: -122: =>start test GETAWAY -122: [00:24:59] test on : 365 molecules done -155/236 Test #122: testGETAWAY ............................ Passed 2.86 sec +69: [20:24:16] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +183: [20:24:16] done +183: [20:24:16] ------------------------------------- +183: [20:24:16] Test3 (stereo options) +146: [20:24:16] --------------------------------- +146: [20:24:16] test sf.net issue 2091974 +146: +146: [20:24:16] --------------------------------- +146: [20:24:16] test sf.net issue 2835784 +146: +146: [20:24:16] --------------------------------- +146: [20:24:16] test sf.net issue 3019283 +146: +146: [20:24:16] --------------------------------- +146: [20:24:16] test sf.net issue 3238580 +146: +146: [20:24:16] --------------------------------- +146: [20:24:16] test sf.net issue 3483968 +146: +146: [20:24:16] --------------------------------- +146: [20:24:16] test github issue 55 +146: +146: [20:24:16] --------------------------------- +146: [20:24:16] test1 +146: +146: [20:24:16] --------------------------------- +146: [20:24:16] test multi-threading +146: +146: building molecules +146: generating reference data +141: [20:24:16] done +141: [20:24:16] ------------------------------------- +141: [20:24:16] Test MMFF multithreading3 +194: .. +194: ---------------------------------------------------------------------- +194: Ran 2 tests in 0.012s +194: +194: OK +184: Randomness seeded to: 4074138428 +184: =============================================================================== +184: All tests passed (171 assertions in 5 test cases) +184: +157/236 Test #184: substructLibraryCatchTest .............. Passed 1.49 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 -148: [00:24:59] Molecule does not have explicit Hs. Consider calling AddHs() -141: [00:24:59] Rep: 80 Mol:2 -141: [00:24:59] Rep: 80 Mol:6 -141: [00:24:59] Rep: 80 Mol:10 -141: [00:24:59] Rep: 80 Mol:14 -141: [00:24:59] Rep: 80 Mol:18 -141: [00:24:59] Rep: 80 Mol:22 -141: [00:24:59] Rep: 80 Mol:26 -141: [00:24:59] Rep: 80 Mol:30 -183: [00:24:59] done -12: .................. -12: ---------------------------------------------------------------------- -12: Ran 18 tests in 3.697s -12: -12: OK -192: .. -192: ---------------------------------------------------------------------- -192: Ran 2 tests in 0.013s -192: -192: OK -183: [00:24:59] ------------------------------------- -183: [00:25:00] Test3 (stereo options) -188: Randomness seeded to: 3345784175 -188: =============================================================================== -188: All tests passed (1475 assertions in 14 test cases) -188: -156/236 Test #188: rgroupCatchTests ....................... Passed 0.83 sec +143: [20:24:16] done +143: [20:24:16] ------------------------------------- +143: [20:24:16] Test UFF multithreading2 +158/236 Test #194: pySLNParse ............................. Passed 0.38 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 -157/236 Test #192: pyMolInterchange ....................... Passed 0.60 sec +192: .. +192: ---------------------------------------------------------------------- +192: Ran 2 tests in 0.026s +192: +192: OK +148: [20:24:16] Molecule does not have explicit Hs. Consider calling AddHs() +183: [20:24:16] Done (stereo options) +183: [20:24:16] ------------------------------------- +183: [20:24:16] Test4 (trusted smiles) +196: ...... +196: ---------------------------------------------------------------------- +196: Ran 6 tests in 0.031s +196: +196: OK +159/236 Test #192: pyMolInterchange ....................... Passed 0.59 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 -117: =>start test 2 WHIM custom -117: [00:25:00] test on : 365 molecules done -158/236 Test #12: pyBV ................................... Passed 4.00 sec +172: .... +172: ---------------------------------------------------------------------- +172: Ran 14 tests in 1.922s +172: +172: OK +160/236 Test #196: pyTestConformerWrap .................... Passed 0.41 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 -196: ...... -196: ---------------------------------------------------------------------- -196: Ran 6 tests in 0.016s -196: -196: OK -194: .. -194: ---------------------------------------------------------------------- -194: Ran 2 tests in 0.012s -194: -194: OK -29: All 191 tests passed -159/236 Test #196: pyTestConformerWrap .................... Passed 0.45 sec +69: [20:24:17] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas +69: [20:24:17] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' +141: [20:24:17] done +141: [20:24:17] ------------------------------------- +141: [20:24:17] Testing github 162: Incorrect SMILES after MMFF parameterization . +141: [20:24:17] done +141: [20:24:17] ------------------------------------- +141: [20:24:17] Testing github 224: crash during MMFF parameterization . +141: [20:24:17] done +141: [20:24:17] ------------------------------------- +141: [20:24:17] Testing github6728: crash due to missing stretch-bend params. +161/236 Test #141: testMMFFForceFieldHelpers .............. Passed 3.51 sec +162/236 Test #172: pyRascalMCES ........................... Passed 2.47 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 -160/236 Test #194: pySLNParse ............................. Passed 0.60 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 -69: [00:25:00] 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: [00:25:00] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -40: [00:25:00] Finished -40: [00:25:00] testing github #1567: Non-canonical result from MolFragmentToSmiles() -40: [00:25:00] Finished -148: [00:25:00] Molecule does not have explicit Hs. Consider calling AddHs() -161/236 Test #40: hanoiTest .............................. Passed 3.88 sec +183: [20:24:17] Done (trusted smiles) +183: [20:24:17] ------------------------------------- +183: [20:24:17] Testing C++ docs +183: [20:24:17] Done (C++ doc tests) +183: [20:24:17] ------------------------------------- +183: [20:24:17] Testing C++ ring query: PatternHolder +183: [20:24:17] Done (C++ ring query tests) +183: [20:24:17] ------------------------------------- +183: [20:24:17] Testing C++ ring query: TautomerPatternHolder +183: [20:24:17] Done (C++ ring query tests) +183: [20:24:17] ------------------------------------- +183: [20:24:17] Add Patterns +69: [20:24:17] Empty atom list: 'M ALS 1 0 F' on line 8. +160: file testHandDrawn-5a.svg gave hash 3327818543U not the expected 1567781555U +160: [20:24:17] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [20:24:17] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +163/236 Test #69: fileParsersTest1 ....................... Passed 4.43 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 -183: [00:25:00] Done (stereo options) -183: [00:25:00] ------------------------------------- -183: [00:25:00] Test4 (trusted smiles) -69: ---------------------------------- -69: ---------------------------------- -69: [00:25:00] -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# 0x0000563C49685FFF in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 4# 0x0000563C496DF3EA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 5# 0x0000563C4965F9A3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 6# 0x00007F4415233CA8 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# 0x0000563C4965FAD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: ---------- -69: **** -69: -69: [00:25:00] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -173: Randomness seeded to: 1078290673 -173: [00:25:00] Writing the enumerated file may take quite some time and result in a large file. -183: [00:25:00] Done (trusted smiles) -183: [00:25:00] ------------------------------------- -183: [00:25:00] Testing C++ docs -183: [00:25:00] Done (C++ doc tests) -183: [00:25:00] ------------------------------------- -183: [00:25:00] Testing C++ ring query: PatternHolder -183: [00:25:00] Done (C++ ring query tests) -183: [00:25:00] ------------------------------------- -183: [00:25:00] Testing C++ ring query: TautomerPatternHolder -183: [00:25:00] Done (C++ ring query tests) -183: [00:25:00] ------------------------------------- -183: [00:25:00] Add Patterns -29: -29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.sdf... -141: [00:25:00] done -141: [00:25:00] ------------------------------------- -141: [00:25:00] Test MMFF multithreading2 -172: .... -172: ---------------------------------------------------------------------- -172: Ran 14 tests in 1.760s -172: -172: OK -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 0.057 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 0.009 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 0.013 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 0.108 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 0.105 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 0.125 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 0.199 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 0.017 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 0.015 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 0.684 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 0.379 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 0.666 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 -163: Time elapsed 0.017 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 -151: 510954157 -151: =============================================================================== -151: All tests passed (73 assertions in 3 test cases) -151: -162/236 Test #151: molAlignCatchTest ...................... Passed 2.89 sec +198: ............. +198: ---------------------------------------------------------------------- +198: Ran 13 tests in 0.027s +198: +198: OK +198: Testing SubstanceGroups wrapper +164/236 Test #198: pyTestSGroups .......................... Passed 0.37 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 -198: ............. -198: ---------------------------------------------------------------------- -198: Ran 13 tests in 0.037s -198: -198: OK -198: Testing SubstanceGroups wrapper -197: [00:25:00] +160: file testHandDrawn-5b.svg gave hash 2125846125U not the expected 66354106U +160: [20:24:17] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [20:24:17] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +204: [20:24:17] Can't kekulize mol. Unkekulized atoms: 3 7 8 9 +197: [20:24:17] 197: 197: **** 197: Pre-condition Violation @@ -30155,23 +30344,23 @@ 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# 0x00007F81CEF6F62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x00007FDD9AD7362C 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# 0x00007F81CCBB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 12# 0x00007F81CCBB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 13# 0x00007F81CCBB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 14# 0x00007F81CCBB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 15# 0x00007F81CCBB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 11# 0x00007FDD989B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 12# 0x00007FDD989B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 13# 0x00007FDD989B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 14# 0x00007FDD989B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 15# 0x00007FDD989B7933 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# 0x00007F81CEF6C3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 21# 0x00007FDD9AD703C6 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 @@ -30203,13 +30392,13 @@ 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# 0x00007F81CF718CA8 in /lib/x86_64-linux-gnu/libc.so.6 +197: 53# 0x00007FDD9B51CCA8 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: .[00:25:00] +197: .[20:24:17] 197: 197: **** 197: Pre-condition Violation @@ -30223,23 +30412,23 @@ 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# 0x00007F81CEF6F62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x00007FDD9AD7362C 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# 0x00007F81CCBB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 12# 0x00007F81CCBB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 13# 0x00007F81CCBB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 14# 0x00007F81CCBB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 15# 0x00007F81CCBB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 11# 0x00007FDD989B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 12# 0x00007FDD989B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 13# 0x00007FDD989B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 14# 0x00007FDD989B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 15# 0x00007FDD989B7933 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# 0x00007F81CEF6C3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 21# 0x00007FDD9AD703C6 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 @@ -30271,254 +30460,55 @@ 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# 0x00007F81CF718CA8 in /lib/x86_64-linux-gnu/libc.so.6 +197: 53# 0x00007FDD9B51CCA8 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: -195: ..............[00:25:00] SMARTS Parse Error: syntax error while parsing: fiib -195: [00:25:00] SMARTS Parse Error: Failed parsing SMARTS 'fiib' for input: 'fiib' -201: [00:25:00] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. -201: [00:25:00] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. -201: [00:25:00] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. -201: .[00:25:00] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. -201: [00:25:00] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. -201: [00:25:00] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. -201: ...[00:25:00] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. -163/236 Test #172: pyRascalMCES ........................... Passed 2.30 sec -201: [00:25:00] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. -201: [00:25:00] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. -201: . -201: ---------------------------------------------------------------------- -201: Ran 5 tests in 0.022s -201: -201: OK -204: [00:25:00] Can't kekulize mol. Unkekulized atoms: 3 7 8 9 -143: [00:25:00] done -143: [00:25:00] ------------------------------------- -143: [00:25:00] Test UFF multithreading2 -202: . -202: ---------------------------------------------------------------------- -202: Ran 1 test in 0.013s -202: -202: OK +143: [20:24:17] done +143: [20:24:17] ------------------------------------- +143: [20:24:17] Test UFF multithreading3 +160: file testHandDrawn-5.png gave hash 2441005674U not the expected 828378555U +204: [20:24:17] Initializing Normalizer +204: [20:24:17] Running Normalizer +204: [20:24:17] Rule applied: BrokenazidetoN=N+=N- +204: [20:24:17] Initializing Normalizer +204: [20:24:17] Running Normalizer +204: [20:24:17] Initializing Normalizer +204: [20:24:17] Running Normalizer +165/236 Test #204: molNormalizeTest ....................... Passed 0.19 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 -195: ....[00:25:00] ERROR: Problems encountered parsing data fields -195: [00:25:00] ERROR: moving to the beginning of the next molecule -195: [00:25:00] ERROR: Problems encountered parsing data fields -195: [00:25:00] ERROR: moving to the beginning of the next molecule -195: [00:25:00] Spurious data before the first property will be ignored -195: [00:25:00] Property will be truncated after the first blank line -195: [00:25:00] Property will be truncated after the first blank line -195: [00:25:00] Property will be truncated after the first blank line -195: [00:25:00] ERROR: Problems encountered parsing data fields -195: [00:25:00] ERROR: moving to the beginning of the next molecule -195: [00:25:00] ERROR: Problems encountered parsing data fields -195: [00:25:00] ERROR: moving to the beginning of the next molecule -195: [00:25:00] Spurious data before the first property will be ignored -195: [00:25:00] Property will be truncated after the first blank line -195: [00:25:00] Property will be truncated after the first blank line -195: [00:25:00] Property will be truncated after the first blank line -195: [00:25:00] ERROR: Problems encountered parsing data fields -195: [00:25:00] ERROR: moving to the beginning of the next molecule -195: [00:25:00] Property will be truncated after the first blank line -195: [00:25:00] ERROR: Problems encountered parsing data fields -195: [00:25:00] ERROR: moving to the beginning of the next molecule -195: [00:25:00] Property will be truncated after the first blank line -164/236 Test #198: pyTestSGroups .......................... Passed 0.59 sec -165/236 Test #201: pyTestPropertyLists .................... Passed 0.56 sec -166/236 Test #202: pyCDXMLTest ............................ Passed 0.54 sec -204: [00:25:00] Initializing Normalizer -204: [00:25:00] Running Normalizer -204: [00:25:00] Rule applied: BrokenazidetoN=N+=N- -204: [00:25:00] Initializing Normalizer -204: [00:25:00] Running Normalizer -204: [00:25:00] Initializing Normalizer -204: [00:25:00] Running Normalizer -167/236 Test #204: molNormalizeTest ....................... Passed 0.31 sec +12: .................. +12: ---------------------------------------------------------------------- +12: Ran 18 tests in 4.717s +12: +12: OK +202: . +202: ---------------------------------------------------------------------- +202: Ran 1 test in 0.024s +202: +202: OK +160: file testBrackets-5a.svg gave hash 279553678U not the expected 1447240271U +166/236 Test #12: pyBV ................................... Passed 4.95 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 +167/236 Test #202: pyCDXMLTest ............................ Passed 0.43 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 -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 -195: .[00:25:00] SMILES Parse Error: syntax error while parsing: fail -195: [00:25:00] SMILES Parse Error: check for mistakes around position 1: -195: [00:25:00] fail -195: [00:25:00] ^ -195: [00:25:00] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' -195: [00:25:00] ERROR: Smiles parse error on line 2 -195: [00:25:00] ERROR: Cannot create molecule from : 'fail' -195: >>> This may result in an infinite loop. It should finish almost instantly -195: <<< OK, it finished. -200: .s. -200: ---------------------------------------------------------------------- -200: Ran 3 tests in 0.207s -200: -200: OK (skipped=1) -200: Testing Smiles and SD MultithreadedMolSupplier -69: [00:25:00] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas -69: [00:25:00] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' -141: [00:25:00] done -141: [00:25:00] ------------------------------------- -141: [00:25:00] Test MMFF multithreading3 -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 -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 0.016 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 0.233 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 0.063 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 -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 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 @@ -30537,350 +30527,106 @@ 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. -69: [00:25:00] Empty atom list: 'M ALS 1 0 F' on line 8. -168/236 Test #205: molValidateTest ........................ Passed 0.19 sec +200: .s. +200: ---------------------------------------------------------------------- +200: Ran 3 tests in 0.346s +200: +200: OK (skipped=1) +200: Testing Smiles and SD MultithreadedMolSupplier +168/236 Test #205: molValidateTest ........................ Passed 0.16 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 +143: [20:24:17] done +143: [20:24:17] ------------------------------------- +143: [20:24:17] Testing GitHubIssue62. +143: [20:24:17] beta-lactam 39.6387 +143: [20:24:17] cyclopropanone 174.698 +143: [20:24:17] aziridine 337.986 +143: [20:24:17] aziridinone 115.248 +143: [20:24:17] isobutene 2.48217 +143: [20:24:17] acetone 1.91788 +160: file testPositionVariation-1b.svg gave hash 3055422087U not the expected 3269244452U +143: [20:24:17] cyclopentanone 10.1648 +143: [20:24:17] cyclopropene 99.4921 +169/236 Test #206: molChargeTest .......................... Passed 0.11 sec +143: [20:24:17] cyclobutene 41.0156 +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 +201: [20:24:17] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. +201: [20:24:17] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. +201: [20:24:17] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. +201: .[20:24:17] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. +201: [20:24:17] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. +201: [20:24:17] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. +201: ...[20:24:17] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. +201: [20:24:17] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. +201: [20:24:17] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. +170/236 Test #200: pyTestMultithreadedMolSupplier ......... Passed 0.68 sec +201: . +201: ---------------------------------------------------------------------- +201: Ran 5 tests in 0.014s +201: +201: OK 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 -169/236 Test #69: fileParsersTest1 ....................... Passed 4.27 sec +143: [20:24:17] cyclopropane 267.236 +143: [20:24:17] gamma-lactam 15.7471 +117: =>start test GETAWAY custom +117: [20:24:17] test on : 365 molecules done +171/236 Test #117: testRDFcustom .......................... Passed 4.57 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 -195: ............[00:25:00] Explicit valence for atom # 1 C, 5, is greater than permitted -143: [00:25:00] done -143: [00:25:00] ------------------------------------- -143: [00:25:00] Test UFF multithreading3 -117: =>start test 1 WHIM custom -117: [00:25:00] test on : 365 molecules done -160: file testHandDrawn-5a.svg gave hash 3327818543U not the expected 1567781555U -160: [00:25:00] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [00:25:00] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. -195: ......[00:25:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -195: [00:25:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -195: [00:25:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -195: [00:25:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -211: Randomness seeded to: 1570327211 -211: 1 Counts line too short: '' on line4 -211: 1 Could not instantiate a valid molecule from input -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)| -211: 8 Molecule has no atoms -211: [00:25:00] Explicit valence for atom # 1 N, 4, is greater than permitted -211: [00:25:00] 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 -160: file testHandDrawn-5b.svg gave hash 2125846125U not the expected 66354106U -170/236 Test #208: molStandardizeSmallTest ................ Passed 0.10 sec +172/236 Test #208: molStandardizeSmallTest ................ Passed 0.11 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: [00:25:00] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [00:25:00] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. -211: 4 Query atom 0 is not allowed -209: [00:25:00] SMARTS Parse Error: syntax error while parsing: [Cl -209: [00:25:00] SMARTS Parse Error: Failed parsing SMARTS '[Cl' for input: '[Cl' -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 -171/236 Test #209: molFragmentTest ........................ Passed 0.11 sec -195: ........[00:25:00] non-ring atom 0 marked aromatic -195: [00:25:00] non-ring atom 0 marked aromatic -195: [00:25:00] -195: -195: **** -195: Range Error -195: idx -195: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp -195: Failed Expression: 12 < 6 -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# 0x00007F916B484A70 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# 0x00007F916DC0662C 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# 0x00007F916B3B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 18# 0x00007F916B3B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 19# 0x00007F916B3B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 20# 0x00007F916B3B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 21# 0x00007F916B3B7933 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# 0x00007F916DC033C6 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# 0x00007F916E3E0CA8 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: [00:25:00] non-ring atom 0 marked aromatic -195: [00:25:00] non-ring atom 0 marked aromatic -195: [00:25:00] -195: -195: **** -195: Range Error -195: idx -195: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp -195: Failed Expression: 12 < 6 -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# 0x00007F916B484A70 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# 0x00007F916DC0662C 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# 0x00007F916B3B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 18# 0x00007F916B3B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 19# 0x00007F916B3B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 20# 0x00007F916B3B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 21# 0x00007F916B3B7933 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# 0x00007F916DC033C6 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# 0x00007F916E3E0CA8 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: +173/236 Test #201: pyTestPropertyLists .................... Passed 0.60 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: 4 Enhanced stereochemistry features are not allowed -211: 8 The radical at atom 0 is not allowed -211: [00:25:00] 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: 32 Atom 0 too close to bond 2 -211: 32 The length of bond 3 between atoms 0 and 3 exceeds a configured limit -211: 64 Atom 0 has 3 explicit substituents and multiple stereo bonds -211: 64 Atom 0 has adjacent stereo bonds with like orientation -211: [00:25:00] 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 -172/236 Test #200: pyTestMultithreadedMolSupplier ......... Passed 0.90 sec +143: [20:24:17] trans-2,3-diphenylcyclopropan-1-one 203.398 +174/236 Test #42: resMolSupplierTest ..................... Passed 5.08 sec +209: [20:24:17] SMARTS Parse Error: syntax error while parsing: [Cl +209: [20:24:17] SMARTS Parse Error: Failed parsing SMARTS '[Cl' for input: '[Cl' +175/236 Test #209: molFragmentTest ........................ Passed 0.08 sec +211: Randomness seeded to: 1622791621 +211: 1 Counts line too short: '' on line4 +211: 1 Could not instantiate a valid molecule from input 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 -173/236 Test #206: molChargeTest .......................... Passed 0.30 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: 32 The length of bond 16 between atoms 16 and 1 exceeds a configured limit -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. -160: file testHandDrawn-5.png gave hash 2441005674U not the expected 828378555U -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. -141: [00:25:01] done -141: [00:25:01] ------------------------------------- -141: [00:25:01] Testing github 162: Incorrect SMILES after MMFF parameterization . -141: [00:25:01] done -141: [00:25:01] ------------------------------------- -141: [00:25:01] Testing github 224: crash during MMFF parameterization . -141: [00:25:01] done -141: [00:25:01] ------------------------------------- -141: [00:25:01] Testing github6728: crash due to missing stretch-bend params. -211: 16777216 The representation of some functional groups was adjusted. -174/236 Test #141: testMMFFForceFieldHelpers .............. Passed 3.65 sec -211: 16777216 The representation of some functional groups was adjusted. -211: 67108864 The protonation state was adjusted. -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 -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. -195: ...............[00:25:01] 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: [00:25:01] 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. -160: file testBrackets-5a.svg gave hash 279553678U not the expected 1447240271U -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. -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. -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 -148: [00:25:01] Molecule does not have explicit Hs. Consider calling AddHs() -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: 3380894664 -216: [00:25:01] can only enumerate SRUs with CONNECT=HT or CONNECT=HH -211: 16777216 The representation of some functional groups was adjusted. -211: [00:25:01] Can't kekulize mol. Unkekulized atoms: 2 3 5 -211: =============================================================================== -211: All tests passed (268 assertions in 5 test cases) -211: -175/236 Test #211: molStandardizePipelineTest ............. Passed 0.32 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 -216: =============================================================================== -216: All tests passed (321 assertions in 16 test cases) -216: -176/236 Test #216: testMolEnumerator ...................... Passed 0.12 sec -195: ..............[00:25:01] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -195: [00:25:01] Explicit valence for atom # 1 C, 5, is greater than permitted -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 -160: file testPositionVariation-1b.svg gave hash 3055422087U not the expected 3269244452U -143: [00:25:01] done -143: [00:25:01] ------------------------------------- -143: [00:25:01] Testing GitHubIssue62. -218: Randomness seeded to: 825470457 -218: [00:25:01] SMARTS Parse Error: syntax error while parsing: *fail -218: [00:25:01] SMARTS Parse Error: Failed parsing SMARTS '*fail' for input: '*fail' -143: [00:25:01] beta-lactam 39.6387 -143: [00:25:01] cyclopropanone 174.698 -143: [00:25:01] aziridine 337.986 -143: [00:25:01] aziridinone 115.248 -197: .[00:25:01] +197: .[20:24:17] 197: 197: **** 197: Range Error @@ -30895,23 +30641,23 @@ 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# 0x00007F81CEF6F62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 6# 0x00007FDD9AD7362C 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# 0x00007F81CCBB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 13# 0x00007F81CCBB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 14# 0x00007F81CCBB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 15# 0x00007F81CCBB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 16# 0x00007F81CCBB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 12# 0x00007FDD989B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 13# 0x00007FDD989B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 14# 0x00007FDD989B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 15# 0x00007FDD989B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 16# 0x00007FDD989B7933 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# 0x00007F81CEF6C3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 22# 0x00007FDD9AD703C6 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 @@ -30943,21 +30689,15 @@ 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# 0x00007F81CF718CA8 in /lib/x86_64-linux-gnu/libc.so.6 +197: 54# 0x00007FDD9B51CCA8 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: -143: [00:25:01] isobutene 2.48217 -197: .[00:25:01] +197: .[20:24:17] 197: 197: **** -218: [00:25:01] no suitable SubstanceGroups found -143: [00:25:01] acetone 1.91788 -218: =============================================================================== -218: All tests passed (195 assertions in 12 test cases) -218: 197: Pre-condition Violation 197: The trajectory must have dimension == 3 197: Violation occurred on line 113 in file ./Code/GraphMol/Trajectory/Trajectory.cpp @@ -30969,23 +30709,23 @@ 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# 0x00007F81CEF6F62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x00007FDD9AD7362C 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# 0x00007F81CCBB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 12# 0x00007F81CCBB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 13# 0x00007F81CCBB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 14# 0x00007F81CCBB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 15# 0x00007F81CCBB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 11# 0x00007FDD989B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 12# 0x00007FDD989B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 13# 0x00007FDD989B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 14# 0x00007FDD989B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 15# 0x00007FDD989B7933 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# 0x00007F81CEF6C3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 21# 0x00007FDD9AD703C6 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 @@ -31017,24 +30757,15 @@ 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# 0x00007F81CF718CA8 in /lib/x86_64-linux-gnu/libc.so.6 +197: 53# 0x00007FDD9B51CCA8 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: ..[00:25:01] +197: ..[20:24:17] 197: 197: **** -143: [00:25:01] cyclopentanone 10.1648 -143: [00:25:01] cyclopropene 99.4921 -177/236 Test #218: testAbbreviations ...................... Passed 0.07 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 197: Pre-condition Violation 197: The trajectory must have dimension == 3 197: Violation occurred on line 154 in file ./Code/GraphMol/Trajectory/Trajectory.cpp @@ -31046,23 +30777,23 @@ 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# 0x00007F81CEF6F62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x00007FDD9AD7362C 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# 0x00007F81CCBB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 12# 0x00007F81CCBB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 13# 0x00007F81CCBB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 14# 0x00007F81CCBB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 15# 0x00007F81CCBB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 11# 0x00007FDD989B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 12# 0x00007FDD989B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 13# 0x00007FDD989B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 14# 0x00007FDD989B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 15# 0x00007FDD989B7933 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# 0x00007F81CEF6C3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 21# 0x00007FDD9AD703C6 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 @@ -31094,17 +30825,15 @@ 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# 0x00007F81CF718CA8 in /lib/x86_64-linux-gnu/libc.so.6 +197: 53# 0x00007FDD9B51CCA8 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: .[00:25:01] +197: .[20:24:17] 197: 197: **** -143: [00:25:01] cyclobutene 41.0156 -143: [00:25:01] cyclopropane 267.236 197: Pre-condition Violation 197: d_pos must not be NULL 197: Violation occurred on line 23 in file ./Code/GraphMol/Trajectory/Trajectory.cpp @@ -31116,23 +30845,23 @@ 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# 0x00007F81CEF6F62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x00007FDD9AD7362C 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# 0x00007F81CCBB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 12# 0x00007F81CCBB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 13# 0x00007F81CCBB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 14# 0x00007F81CCBB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 15# 0x00007F81CCBB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 11# 0x00007FDD989B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 12# 0x00007FDD989B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 13# 0x00007FDD989B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 14# 0x00007FDD989B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 15# 0x00007FDD989B7933 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# 0x00007F81CEF6C3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 21# 0x00007FDD9AD703C6 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 @@ -31164,13 +30893,13 @@ 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# 0x00007F81CF718CA8 in /lib/x86_64-linux-gnu/libc.so.6 +197: 53# 0x00007FDD9B51CCA8 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: [00:25:01] +197: [20:24:17] 197: 197: **** 197: Pre-condition Violation @@ -31184,23 +30913,23 @@ 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# 0x00007F81CEF6F62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x00007FDD9AD7362C 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# 0x00007F81CCBB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 12# 0x00007F81CCBB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 13# 0x00007F81CCBB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 14# 0x00007F81CCBB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 15# 0x00007F81CCBB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 11# 0x00007FDD989B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 12# 0x00007FDD989B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 13# 0x00007FDD989B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 14# 0x00007FDD989B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 15# 0x00007FDD989B7933 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# 0x00007F81CEF6C3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 21# 0x00007FDD9AD703C6 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 @@ -31232,14 +30961,13 @@ 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# 0x00007F81CF718CA8 in /lib/x86_64-linux-gnu/libc.so.6 +197: 53# 0x00007FDD9B51CCA8 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: -143: [00:25:01] gamma-lactam 15.7471 -197: .[00:25:01] +197: .[20:24:17] 197: 197: **** 197: Range Error @@ -31254,23 +30982,23 @@ 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# 0x00007F81CEF6F62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 6# 0x00007FDD9AD7362C 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# 0x00007F81CCBB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 13# 0x00007F81CCBB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 14# 0x00007F81CCBB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 15# 0x00007F81CCBB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 16# 0x00007F81CCBB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 12# 0x00007FDD989B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 13# 0x00007FDD989B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 14# 0x00007FDD989B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 15# 0x00007FDD989B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 16# 0x00007FDD989B7933 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# 0x00007F81CEF6C3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 22# 0x00007FDD9AD703C6 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 @@ -31302,13 +31030,13 @@ 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# 0x00007F81CF718CA8 in /lib/x86_64-linux-gnu/libc.so.6 +197: 54# 0x00007FDD9B51CCA8 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: [00:25:01] +197: [20:24:17] 197: 197: **** 197: Range Error @@ -31322,23 +31050,23 @@ 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# 0x00007F81CEF6F62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x00007FDD9AD7362C 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# 0x00007F81CCBB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 12# 0x00007F81CCBB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 13# 0x00007F81CCBB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 14# 0x00007F81CCBB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 15# 0x00007F81CCBB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 11# 0x00007FDD989B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 12# 0x00007FDD989B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 13# 0x00007FDD989B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 14# 0x00007FDD989B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 15# 0x00007FDD989B7933 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# 0x00007F81CEF6C3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 21# 0x00007FDD9AD703C6 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 @@ -31370,14 +31098,13 @@ 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# 0x00007F81CF718CA8 in /lib/x86_64-linux-gnu/libc.so.6 +197: 53# 0x00007FDD9B51CCA8 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: -148: [00:25:01] Molecule does not have explicit Hs. Consider calling AddHs() -197: .[00:25:01] +197: .[20:24:17] 197: 197: **** 197: Range Error @@ -31392,23 +31119,23 @@ 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# 0x00007F81CEF6F62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 6# 0x00007FDD9AD7362C 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# 0x00007F81CCBB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 13# 0x00007F81CCBB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 14# 0x00007F81CCBB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 15# 0x00007F81CCBB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 16# 0x00007F81CCBB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 12# 0x00007FDD989B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 13# 0x00007FDD989B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 14# 0x00007FDD989B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 15# 0x00007FDD989B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 16# 0x00007FDD989B7933 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# 0x00007F81CEF6C3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 22# 0x00007FDD9AD703C6 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 @@ -31440,13 +31167,13 @@ 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# 0x00007F81CF718CA8 in /lib/x86_64-linux-gnu/libc.so.6 +197: 54# 0x00007FDD9B51CCA8 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: [00:25:01] +197: [20:24:17] 197: 197: **** 197: Pre-condition Violation @@ -31460,23 +31187,23 @@ 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# 0x00007F81CEF6F62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x00007FDD9AD7362C 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# 0x00007F81CCBB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 12# 0x00007F81CCBB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 13# 0x00007F81CCBB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 14# 0x00007F81CCBB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 15# 0x00007F81CCBB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 11# 0x00007FDD989B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 12# 0x00007FDD989B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 13# 0x00007FDD989B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 14# 0x00007FDD989B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 15# 0x00007FDD989B7933 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# 0x00007F81CEF6C3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 21# 0x00007FDD9AD703C6 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 @@ -31508,15 +31235,30 @@ 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# 0x00007F81CF718CA8 in /lib/x86_64-linux-gnu/libc.so.6 +197: 53# 0x00007FDD9B51CCA8 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: [00:25:01] +197: [20:24:17] 197: 197: **** +211: 8 Molecule has no atoms +211: [20:24:17] Explicit valence for atom # 1 N, 4, is greater than permitted +211: [20:24:17] 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 +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 197: Pre-condition Violation 197: d_dimension must be == 2 197: Violation occurred on line 25 in file ./Code/GraphMol/Trajectory/Trajectory.cpp @@ -31528,23 +31270,23 @@ 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# 0x00007F81CEF6F62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x00007FDD9AD7362C 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# 0x00007F81CCBB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 12# 0x00007F81CCBB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 13# 0x00007F81CCBB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 14# 0x00007F81CCBB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 15# 0x00007F81CCBB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 11# 0x00007FDD989B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 12# 0x00007FDD989B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 13# 0x00007FDD989B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 14# 0x00007FDD989B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 15# 0x00007FDD989B7933 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# 0x00007F81CEF6C3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 21# 0x00007FDD9AD703C6 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 @@ -31576,7 +31318,7 @@ 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# 0x00007F81CF718CA8 in /lib/x86_64-linux-gnu/libc.so.6 +197: 53# 0x00007FDD9B51CCA8 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: ---------- @@ -31584,105 +31326,519 @@ 197: 197: . 197: ---------------------------------------------------------------------- -197: Ran 9 tests in 0.852s +197: Ran 9 tests in 0.482s 197: 197: OK 197: Testing Trajectory wrapper -143: [00:25:01] trans-2,3-diphenylcyclopropan-1-one 203.398 -178/236 Test #197: pyTestTrajectory ....................... Passed 1.36 sec +211: 4 Enhanced stereochemistry features are not allowed +211: 8 The radical at atom 0 is not allowed +211: [20:24:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +143: [20:24:17] cis-2,3-diphenylcyclopropan-1-one 206.852 +211: 16 The molecule includes non-null Z coordinates +211: 32 Atom 0 too close to bond 2 +195: ..............[20:24:17] SMARTS Parse Error: syntax error while parsing: fiib +195: [20:24:17] SMARTS Parse Error: Failed parsing SMARTS 'fiib' for input: 'fiib' +211: 32 The length of bond 3 between atoms 0 and 3 exceeds a configured limit +211: 64 Atom 0 has 3 explicit substituents and multiple stereo bonds +211: 64 Atom 0 has adjacent stereo bonds with like orientation +211: [20:24:17] 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 +143: [20:24:17] 2,3-diphenylcyclopropa-2-en-1-one 20.0443 +195: ....[20:24:17] ERROR: Problems encountered parsing data fields +195: [20:24:17] ERROR: moving to the beginning of the next molecule +195: [20:24:17] ERROR: Problems encountered parsing data fields +195: [20:24:17] ERROR: moving to the beginning of the next molecule +195: [20:24:17] Spurious data before the first property will be ignored +195: [20:24:17] Property will be truncated after the first blank line +195: [20:24:17] Property will be truncated after the first blank line +195: [20:24:17] Property will be truncated after the first blank line +195: [20:24:17] ERROR: Problems encountered parsing data fields +195: [20:24:17] ERROR: moving to the beginning of the next molecule +195: [20:24:17] ERROR: Problems encountered parsing data fields +195: [20:24:17] ERROR: moving to the beginning of the next molecule +195: [20:24:17] Spurious data before the first property will be ignored +195: [20:24:17] Property will be truncated after the first blank line +195: [20:24:17] Property will be truncated after the first blank line +195: [20:24:17] Property will be truncated after the first blank line +195: [20:24:17] ERROR: Problems encountered parsing data fields +195: [20:24:17] ERROR: moving to the beginning of the next molecule +195: [20:24:17] Property will be truncated after the first blank line +195: [20:24:17] ERROR: Problems encountered parsing data fields +195: [20:24:17] ERROR: moving to the beginning of the next molecule +195: [20:24:17] Property will be truncated after the first blank line +143: [20:24:17] cyclopropylidencyclobutane 218.879 +176/236 Test #197: pyTestTrajectory ....................... Passed 1.00 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 +169: ......... +169: ---------------------------------------------------------------------- +169: Ran 9 tests in 2.913s +169: +169: OK +211: 32 The length of bond 16 between atoms 16 and 1 exceeds a configured limit +195: .[20:24:17] SMILES Parse Error: syntax error while parsing: fail +195: [20:24:17] SMILES Parse Error: check for mistakes around position 1: +195: [20:24:17] fail +195: [20:24:17] ^ +195: [20:24:17] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' +195: [20:24:17] ERROR: Smiles parse error on line 2 +195: [20:24:17] ERROR: Cannot create molecule from : 'fail' +195: >>> This may result in an infinite loop. It should finish almost instantly +195: <<< OK, it finished. +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. +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. +195: ............[20:24:17] Explicit valence for atom # 1 C, 5, is greater than permitted +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. +177/236 Test #169: pyMMPA ................................. Passed 3.26 sec +211: 16777216 The representation of some functional groups was adjusted. +211: 67108864 The protonation state was adjusted. +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 +211: 16777216 The representation of some functional groups was adjusted. +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. +143: [20:24:17] diphenylmethylidencyclobutane 79.6139 +211: 67108864 The protonation state was adjusted. +216: Randomness seeded to: 793826393 +216: [20:24:17] can only enumerate SRUs with CONNECT=HT or CONNECT=HH +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: [20:24:17] done +143: [20:24:17] ------------------------------------- +143: [20:24:17] Test Github Issue 613: UFF Atom type not properly assigned to lanthanides. +143: [20:24:17] done +143: [20:24:17] ------------------------------------- +143: [20:24:17] Test square planar complexes +143: [20:24:17] done +143: [20:24:17] ------------------------------------- +143: [20:24:17] Test octahedral complexes +143: [20:24:17] done +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. +178/236 Test #143: testUFFForceFieldHelpers ............... Passed 4.27 sec +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. +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 +163: [20:24:17] The provided InitialSeed is not an MCS and will be ignored +216: =============================================================================== +216: All tests passed (321 assertions in 16 test cases) +216: +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 +179/236 Test #216: testMolEnumerator ...................... Passed 0.14 sec +211: 16777216 The representation of some functional groups was adjusted. +211: [20:24:17] Can't kekulize mol. Unkekulized atoms: 2 3 5 +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 +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 +160: [20:24:17] unrecognized bond typefile testGithub4238_1.png gave hash 2704600159U not the expected 2623427676U +128: [20:24:17] done +128: [20:24:17] ------------------------------------- +128: [20:24:17] Test GitHub Issue 258: Bad pattern fingerprint for query molecule +128: [20:24:17] done +128: [20:24:17] ------------------------------------- +128: [20:24:17] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. +128: [20:24:17] DEPRECATION WARNING: please use AtomPairGenerator +128: [20:24:17] DEPRECATION WARNING: please use AtomPairGenerator +128: [20:24:17] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:17] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:17] done +128: [20:24:17] ------------------------------------- +128: [20:24:17] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints +128: [20:24:17] done +128: [20:24:17] ------------------------------------- +128: [20:24:17] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 +128: [20:24:17] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:17] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:17] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:17] done +128: [20:24:17] ------------------------------------- +128: [20:24:17] Test unfolded version of RDKFP +128: [20:24:17] ------------------------------------- +128: [20:24:17] Test bitinfo of RDKFP +128: 562: [ 2 ], +128: 709: [ 0 1 ], +128: 1118: [ 0 1 2 ], +128: 1183: [ 1 2 ], +128: 1233: [ 0 1 2 ], +128: 1308: [ 0 ], [ 1 ], +128: 1339: [ 2 ], +128: 1728: [ 1 2 ], +128: 1772: [ 0 ], [ 1 ], +128: 1813: [ 0 1 ], +128: ------------ +128: [20:24:17] ------------------------------------- +128: [20:24:17] Single atoms setting radius 1 bits in Morgan fingerprints +128: [20:24:17] done +128: [20:24:17] ------------------------------------- +128: [20:24:17] Github #879: Pattern fingerprint should set bits for single-atom fragments. +128: [20:24:17] done +128: [20:24:17] ------------------------------------- +128: [20:24:17] Github #1496: Pattern fingerprint setting bad bits for degree zero atoms +128: [20:24:17] done +128: [20:24:17] ------------------------------------- +128: [20:24:17] Github #1793: Fingerprint segfaults with branchedPaths=False and useHs=False +128: [20:24:17] done +128: [20:24:17] ------------------------------------- +128: [20:24:17] Github #1993: fingerprinters that use R/S labels should force a call to assignStereochemistry() if it hasn't already been called +128: [20:24:17] DEPRECATION WARNING: please use AtomPairGenerator +128: [20:24:17] DEPRECATION WARNING: please use AtomPairGenerator +128: [20:24:17] DEPRECATION WARNING: please use AtomPairGenerator +128: [20:24:17] DEPRECATION WARNING: please use AtomPairGenerator +211: =============================================================================== +211: All tests passed (268 assertions in 5 test cases) +211: +128: [20:24:17] DEPRECATION WARNING: please use AtomPairGenerator +128: [20:24:17] DEPRECATION WARNING: please use AtomPairGenerator +128: [20:24:17] DEPRECATION WARNING: please use AtomPairGenerator +128: [20:24:17] DEPRECATION WARNING: please use AtomPairGenerator +128: [20:24:17] DEPRECATION WARNING: please use AtomPairGenerator +128: [20:24:17] DEPRECATION WARNING: please use AtomPairGenerator +128: [20:24:17] DEPRECATION WARNING: please use AtomPairGenerator +128: [20:24:17] DEPRECATION WARNING: please use AtomPairGenerator +128: [20:24:17] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:17] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:17] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:17] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:17] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:17] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:17] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:17] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:17] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:17] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:17] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:17] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [20:24:17] done +128: [20:24:17] ------------------------------------- +128: [20:24:17] Github #2115: BitInfo not complete for RDKFingerprint +128: [20:24:17] done +128: [20:24:17] ------------------------------------- +128: [20:24:17] Github #3723: Fingerprint crash for mols with Zero order bonds +128: [20:24:17] done +195: ......[20:24:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +195: [20:24:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +195: [20:24:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +195: [20:24:17] 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)| +148: [20:24:17] Molecule does not have explicit Hs. Consider calling AddHs() +180/236 Test #211: molStandardizePipelineTest ............. Passed 0.30 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 -214: ....... -214: ---------------------------------------------------------------------- -214: Ran 7 tests in 0.056s -214: -214: OK -143: [00:25:01] cis-2,3-diphenylcyclopropan-1-one 206.852 -210: Randomness seeded to: 2691322691 -210: * - * - * - * m1 -210: * - * - * - * m2 -210: * - * - * - * m1 -210: * - * - * - * m2 -179/236 Test #214: pyScaffoldNetwork ...................... Passed 0.38 sec +181/236 Test #128: testFingerprints ....................... Passed 4.65 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 -210: [00:25:01] Can't kekulize mol. Unkekulized atoms: 3 7 -143: [00:25:01] 2,3-diphenylcyclopropa-2-en-1-one 20.0443 -210: [00:25:01] Can't kekulize mol. Unkekulized atoms: 3 8 -143: [00:25:01] cyclopropylidencyclobutane 218.879 +160: file testGithub4323_1.png gave hash 1936109620U not the expected 3075787867U +210: Randomness seeded to: 1005750222 +210: * - * - * - * m1 +218: Randomness seeded to: 3741810469 +218: [20:24:18] SMARTS Parse Error: syntax error while parsing: *fail +218: [20:24:18] SMARTS Parse Error: Failed parsing SMARTS '*fail' for input: '*fail' +210: * - * - * - * m2 215: . 215: ---------------------------------------------------------------------- -215: Ran 1 test in 0.021s +215: Ran 1 test in 0.017s 215: 215: OK -210: [00:25:01] Can't kekulize mol. Unkekulized atoms: 2 3 4 -160: [00:25:01] unrecognized bond typefile testGithub4238_1.png gave hash 2704600159U not the expected 2623427676U -148: [00:25:01] Molecule does not have explicit Hs. Consider calling AddHs() -169: ......... -169: ---------------------------------------------------------------------- -169: Ran 9 tests in 2.905s -169: -169: OK -160: file testGithub4323_1.png gave hash 1936109620U not the expected 3075787867U -180/236 Test #215: pyScaffoldNetworkPickling .............. Passed 0.44 sec +210: * - * - * - * m1 +210: * - * - * - * m2 +195: ........[20:24:18] non-ring atom 0 marked aromatic +195: [20:24:18] non-ring atom 0 marked aromatic +195: [20:24:18] +195: +195: **** +210: [20:24:18] Can't kekulize mol. Unkekulized atoms: 3 7 +218: [20:24:18] no suitable SubstanceGroups found +218: =============================================================================== +218: All tests passed (195 assertions in 12 test cases) +218: +195: Range Error +195: idx +195: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp +195: Failed Expression: 12 < 6 +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# 0x00007FB3B6284A70 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# 0x00007FB3B89D062C 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# 0x00007FB3B61B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 18# 0x00007FB3B61B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 19# 0x00007FB3B61B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 20# 0x00007FB3B61B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 21# 0x00007FB3B61B7933 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# 0x00007FB3B89CD3C6 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# 0x00007FB3B91AACA8 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: [20:24:18] non-ring atom 0 marked aromatic +195: [20:24:18] non-ring atom 0 marked aromatic +195: [20:24:18] +195: +195: **** +195: Range Error +195: idx +195: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp +195: Failed Expression: 12 < 6 +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# 0x00007FB3B6284A70 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# 0x00007FB3B89D062C 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# 0x00007FB3B61B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 18# 0x00007FB3B61B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 19# 0x00007FB3B61B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 20# 0x00007FB3B61B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 21# 0x00007FB3B61B7933 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# 0x00007FB3B89CD3C6 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# 0x00007FB3B91AACA8 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: +182/236 Test #218: testAbbreviations ...................... Passed 0.12 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 -143: [00:25:01] diphenylmethylidencyclobutane 79.6139 -143: [00:25:01] done -143: [00:25:01] ------------------------------------- -143: [00:25:01] Test Github Issue 613: UFF Atom type not properly assigned to lanthanides. -143: [00:25:01] done -143: [00:25:01] ------------------------------------- -143: [00:25:01] Test square planar complexes -143: [00:25:01] done -143: [00:25:01] ------------------------------------- -143: [00:25:01] Test octahedral complexes -143: [00:25:01] done -217: ... -217: ---------------------------------------------------------------------- -217: Ran 3 tests in 0.015s -217: -217: OK -181/236 Test #143: testUFFForceFieldHelpers ............... Passed 4.03 sec +210: [20:24:18] Can't kekulize mol. Unkekulized atoms: 3 8 +210: [20:24:18] Can't kekulize mol. Unkekulized atoms: 2 3 4 +183/236 Test #215: pyScaffoldNetworkPickling .............. Passed 0.35 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 -182/236 Test #169: pyMMPA ................................. Passed 3.39 sec +148: [20:24:18] 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... +195: ...............[20:24:18] 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: [20:24:18] 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. +214: ....... +214: ---------------------------------------------------------------------- +214: Ran 7 tests in 0.052s +214: +214: OK +217: ... +217: ---------------------------------------------------------------------- +217: Ran 3 tests in 0.016s +217: +217: OK +184/236 Test #214: pyScaffoldNetwork ...................... Passed 0.46 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 -183/236 Test #217: pyMolEnumerator ........................ Passed 0.37 sec +29: All 191 tests passed +160: file testGithub4323_3.png gave hash 1732257634U not the expected 381907253U +160: [20:24:18] FIELDDISP info not found for DAT SGroup which isn't associated with an atom. SGroup will not be rendered. +220: Randomness seeded to: 3895874439 +220: =============================================================================== +220: All tests passed (486 assertions in 10 test cases) +220: +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 +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 +160: file testGithub4764.sz1.png gave hash 517897906U not the expected 2179222277U +160: file testGithub4764.sz2.png gave hash 2568067924U not the expected 444262090U +160: file testGithub4764.sz3.png gave hash 2910755141U not the expected 3567162200U +185/236 Test #220: generalizedSubstructCatch .............. Passed 1.29 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 -148: [00:25:01] Molecule does not have explicit Hs. Consider calling AddHs() -219: ....... -219: ---------------------------------------------------------------------- -219: Ran 7 tests in 0.021s -219: -219: OK -184/236 Test #219: pyAbbreviations ........................ Passed 0.38 sec +148: [20:24:19] Molecule does not have explicit Hs. Consider calling AddHs() +186/236 Test #217: pyMolEnumerator ........................ Passed 1.42 sec test 226 Start 226: testQuery @@ -31706,23 +31862,13 @@ 226: XOr 226: pointer and copy foo 226: Set2 -185/236 Test #226: testQuery .............................. Passed 0.01 sec +187/236 Test #226: testQuery .............................. Passed 0.01 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 -224: Randomness seeded to: 1850435766 -224: =============================================================================== -224: All tests passed (27926 assertions in 8 test cases) -224: -220: Randomness seeded to: 1296502859 -220: =============================================================================== -220: All tests passed (486 assertions in 10 test cases) -220: -186/236 Test #220: generalizedSubstructCatch .............. Passed 0.33 sec -187/236 Test #224: testMIF ................................ Passed 0.14 sec 227: ------------------------------------- 227: Basics for ExplicitFeatures. 227: done @@ -31732,25 +31878,13 @@ 227: ------------------------------------- 227: ExplicitFeatures 2D, string type. 227: done -188/236 Test #227: testBaseFeatures ....................... Passed 0.02 sec +188/236 Test #227: testBaseFeatures ....................... Passed 0.00 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 -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 -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 228: 1.68022e+08 228: 1.73149e+08 228: 1.05549e+08 @@ -31796,153 +31930,133 @@ 228: 9.49496e+07 228: 2.25618e+08 228: 1.30219e+08 -189/236 Test #228: testMatCalc ............................ Passed 0.02 sec +189/236 Test #228: testMatCalc ............................ Passed 0.01 sec +195: ..............[20:24:19] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +195: [20:24:19] Explicit valence for atom # 1 C, 5, is greater than permitted +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 +160: file github5383_1.svg gave hash 4241964660U not the expected 1815941817U +219: ....... +219: ---------------------------------------------------------------------- +219: Ran 7 tests in 0.021s +219: +219: OK +160: file github5383_2.svg gave hash 2560846108U not the expected 0U +29: +29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.sdf... +160: file github5383_1.png gave hash 1118153320U not the expected 2893520928U +160: file acs1996_1.png gave hash 1014030062U not the expected 2329725800U +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 +224: Randomness seeded to: 3206557846 +224: =============================================================================== +224: All tests passed (27926 assertions in 8 test cases) +224: +190/236 Test #219: pyAbbreviations ........................ Passed 1.44 sec +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 +207: [20:24:19] Tautomer enumeration stopped at 292 tautomers: max transforms reached +171: Randomness seeded to: 3273850090 +171: /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/data/chembl_1907596.smi +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 +191/236 Test #224: testMIF ................................ Passed 1.25 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 -230: [00:25:01] ------------------------------------- -230: [00:25:01] Testing github issue 1421: MaxMinPicker picking non-existent element. -230: [00:25:01] Done -230: [00:25:01] ------------------------------------- -230: [00:25:01] Testing github issue 2245: MinMax Diversity picker seeding shows deterministic / non-random behaviour. -230: [00:25:01] Done -190/236 Test #230: testSimDivPickers ...................... Passed 0.01 sec +230: [20:24:19] ------------------------------------- +230: [20:24:19] Testing github issue 1421: MaxMinPicker picking non-existent element. +230: [20:24:19] Done +230: [20:24:19] ------------------------------------- +230: [20:24:19] Testing github issue 2245: MinMax Diversity picker seeding shows deterministic / non-random behaviour. +230: [20:24:19] Done +125: =============================================================================== +125: All tests passed (515 assertions in 10 test cases) +125: +192/236 Test #230: testSimDivPickers ...................... Passed 0.01 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 -195: ............................[00:25:01] unable to set wavy bonds for double bonds: 3 -191/236 Test #203: molStandardizeTest ..................... Passed 1.52 sec +146: validating reference data +193/236 Test #125: descriptorsTestCatch ................... Passed 6.19 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 -195: .............[00:25:01] -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# 0x00007F916DC0662C 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# 0x00007F916B3B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 18# 0x00007F916B3B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 19# 0x00007F916B3B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 20# 0x00007F916B3B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 21# 0x00007F916B3B7933 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# 0x00007F916DC033C6 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# 0x00007F916E3E0CA8 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: -207: [00:25:01] Tautomer enumeration stopped at 292 tautomers: max transforms reached -231: Randomness seeded to: 4072484216 +160: file acs1996_2.png gave hash 1604110899U not the expected 2996350718U +160: file acs1996_3.svg gave hash 3058522544U not the expected 879041204U +231: Randomness seeded to: 2053763659 231: =============================================================================== 231: All tests passed (21267 assertions in 1 test case) 231: -192/236 Test #231: pickersTestsCatch ...................... Passed 0.10 sec +194/236 Test #203: molStandardizeTest ..................... Passed 2.37 sec +195/236 Test #231: pickersTestsCatch ...................... Passed 0.09 sec +160: [20:24:19] 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. 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 -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 -148: [00:25:01] Molecule does not have explicit Hs. Consider calling AddHs() -160: file testGithub4323_3.png gave hash 1732257634U not the expected 381907253U -160: [00:25:01] FIELDDISP info not found for DAT SGroup which isn't associated with an atom. SGroup will not be rendered. -146: validating reference data -221: ....... -221: ---------------------------------------------------------------------- -221: Ran 7 tests in 0.194s -221: -221: OK -225: ....... -225: ---------------------------------------------------------------------- -225: Ran 7 tests in 0.093s -225: -225: OK -225: Testing MIF wrapper -194/236 Test #221: pyGeneralizedSubstruct ................. Passed 0.59 sec +234: ----------------------------------------- +234: Test1 +234: Done +196/236 Test #234: testChemicalFeatures ................... Passed 0.02 sec +148: [20:24:19] Molecule does not have explicit Hs. Consider calling AddHs() 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 -233: ..[00:25:01] +160: file bond_highlights_8.svg gave hash 3610726614U not the expected 3119784980U +212: .....[20:24:19] Tautomer enumeration stopped at 292 tautomers: max transforms reached +225: ....... +225: ---------------------------------------------------------------------- +225: Ran 7 tests in 0.084s +225: +225: OK +225: Testing MIF wrapper +221: ....... +221: ---------------------------------------------------------------------- +221: Ran 7 tests in 0.174s +221: +221: OK +189: .................... +189: ---------------------------------------------------------------------- +189: Ran 20 tests in 3.136s +189: +189: OK +197/236 Test #225: pyMIF .................................. Passed 0.40 sec +212: [20:24:19] Tautomer enumeration stopped at 50 tautomers: max tautomers reached +198/236 Test #221: pyGeneralizedSubstruct ................. Passed 1.69 sec +199/236 Test #189: pyRGroupDecomposition .................. Passed 3.71 sec +233: ..[20:24:19] 233: 233: **** 233: Invariant Violation @@ -31957,14 +32071,14 @@ 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# 0x00007F54DD8D962C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +233: 6# 0x00007F405BE9162C 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# 0x00007F54DD8D63C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +233: 13# 0x00007F405BE8E3C6 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 @@ -31996,7 +32110,7 @@ 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# 0x00007F54DEAE8CA8 in /lib/x86_64-linux-gnu/libc.so.6 +233: 45# 0x00007F405D09FCA8 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: ---------- @@ -32004,375 +32118,206 @@ 233: 233: ... 233: ---------------------------------------------------------------------- -233: Ran 5 tests in 0.024s +233: Ran 5 tests in 0.026s 233: 233: OK -148: [00:25:01] Molecule does not have explicit Hs. Consider calling AddHs() +232: [20:24:19] the useCache argument is deprecated and ignored +200/236 Test #233: pyRanker ............................... Passed 0.33 sec +195: ............................[20:24:19] unable to set wavy bonds for double bonds: 3 +148: [20:24:19] Molecule does not have explicit Hs. Consider calling AddHs() +207: [20:24:19] Tautomer enumeration stopped at 292 tautomers: max transforms reached 223: .. 223: ---------------------------------------------------------------------- -223: Ran 2 tests in 0.235s +223: Ran 2 tests in 0.519s 223: 223: OK -195/236 Test #225: pyMIF .................................. Passed 0.50 sec -196/236 Test #233: pyRanker ............................... Passed 0.33 sec -232: [00:25:02] the useCache argument is deprecated and ignored -189: .................... -189: ---------------------------------------------------------------------- -189: Ran 20 tests in 2.469s -189: -189: OK +232: ...[20:24:19] the useCache argument is deprecated and ignored +232: [20:24:19] the useCache argument is deprecated and ignored 235: .. 235: ---------------------------------------------------------------------- -235: Ran 2 tests in 0.001s +235: Ran 2 tests in 0.002s 235: 235: OK 235: Testing ChemicalFeatures Wrapper code: -212: .....[00:25:02] Tautomer enumeration stopped at 292 tautomers: max transforms reached -197/236 Test #189: pyRGroupDecomposition .................. Passed 2.89 sec -198/236 Test #223: pyMolProcessing ........................ Passed 0.65 sec -199/236 Test #235: pyFeatures ............................. Passed 0.38 sec -232: ...[00:25:02] the useCache argument is deprecated and ignored -171: Randomness seeded to: 1069197233 -171: /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/data/chembl_1907596.smi -232: [00:25:02] the useCache argument is deprecated and ignored -232: .[00:25:02] the useCache argument is deprecated and ignored -212: [00:25:02] Tautomer enumeration stopped at 50 tautomers: max tautomers reached -207: [00:25:02] Tautomer enumeration stopped at 292 tautomers: max transforms reached -128: [00:25:02] done -128: [00:25:02] ------------------------------------- -128: [00:25:02] Test GitHub Issue 258: Bad pattern fingerprint for query molecule -128: [00:25:02] done -128: [00:25:02] ------------------------------------- -128: [00:25:02] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. -128: [00:25:02] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:25:02] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:25:02] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:25:02] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:25:02] done -128: [00:25:02] ------------------------------------- -128: [00:25:02] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints -128: [00:25:02] done -128: [00:25:02] ------------------------------------- -128: [00:25:02] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 -128: [00:25:02] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:25:02] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:25:02] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:25:02] done -128: [00:25:02] ------------------------------------- -128: [00:25:02] Test unfolded version of RDKFP -128: [00:25:02] ------------------------------------- -128: [00:25:02] Test bitinfo of RDKFP -128: 562: [ 2 ], -128: 709: [ 0 1 ], -128: 1118: [ 0 1 2 ], -128: 1183: [ 1 2 ], -128: 1233: [ 0 1 2 ], -128: 1308: [ 0 ], [ 1 ], -128: 1339: [ 2 ], -128: 1728: [ 1 2 ], -128: 1772: [ 0 ], [ 1 ], -128: 1813: [ 0 1 ], -128: ------------ -128: [00:25:02] ------------------------------------- -128: [00:25:02] Single atoms setting radius 1 bits in Morgan fingerprints -128: [00:25:02] done -128: [00:25:02] ------------------------------------- -128: [00:25:02] Github #879: Pattern fingerprint should set bits for single-atom fragments. -128: [00:25:02] done -128: [00:25:02] ------------------------------------- -128: [00:25:02] Github #1496: Pattern fingerprint setting bad bits for degree zero atoms -128: [00:25:02] done -128: [00:25:02] ------------------------------------- -128: [00:25:02] Github #1793: Fingerprint segfaults with branchedPaths=False and useHs=False -128: [00:25:02] done -128: [00:25:02] ------------------------------------- -128: [00:25:02] Github #1993: fingerprinters that use R/S labels should force a call to assignStereochemistry() if it hasn't already been called -128: [00:25:02] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:25:02] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:25:02] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:25:02] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:25:02] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:25:02] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:25:02] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:25:02] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:25:02] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:25:02] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:25:02] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:25:02] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:25:02] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:25:02] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:25:02] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:25:02] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:25:02] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:25:02] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:25:02] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:25:02] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:25:02] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:25:02] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:25:02] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:25:02] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:25:02] done -128: [00:25:02] ------------------------------------- -128: [00:25:02] Github #2115: BitInfo not complete for RDKFingerprint -128: [00:25:02] done -128: [00:25:02] ------------------------------------- -128: [00:25:02] Github #3723: Fingerprint crash for mols with Zero order bonds -128: [00:25:02] done -200/236 Test #128: testFingerprints ....................... Passed 5.20 sec -207: [00:25:02] Tautomer enumeration stopped at 50 tautomers: max tautomers reached +232: .[20:24:19] the useCache argument is deprecated and ignored +195: .............[20:24:19] +195: +195: **** +160: file test_github6112.svg gave hash 3865338574U not the expected 3278777629U +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# 0x00007FB3B89D062C 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# 0x00007FB3B61B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 18# 0x00007FB3B61B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 19# 0x00007FB3B61B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 20# 0x00007FB3B61B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 21# 0x00007FB3B61B7933 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# 0x00007FB3B89CD3C6 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# 0x00007FB3B91AACA8 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: +207: [20:24:19] Tautomer enumeration stopped at 50 tautomers: max tautomers reached +186: iterative +212: .[20:24:19] Tautomer enumeration stopped at 33 tautomers: canceled +212: Enumeration was canceled due to timeout (50 ms) +201/236 Test #223: pyMolProcessing ........................ Passed 1.89 sec +202/236 Test #235: pyFeatures ............................. Passed 0.42 sec 229: ..... 229: ---------------------------------------------------------------------- -229: Ran 5 tests in 0.332s +229: Ran 5 tests in 0.427s 229: 229: OK -201/236 Test #229: pyMatCalc .............................. Passed 0.73 sec -212: .[00:25:02] Tautomer enumeration stopped at 53 tautomers: canceled -212: Enumeration was canceled due to timeout (50 ms) -160: file testFlexiCanvas.2a.png gave hash 1389326866U not the expected 2609920321U -160: file testFlexiCanvas.2b.png gave hash 614693993U not the expected 3615599154U -207: [00:25:02] Tautomer enumeration stopped at 34 tautomers: canceled -207: Enumeration was canceled due to timeout (50 ms) -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 -160: file testFlexiCanvas.3.svg gave hash 236661785U not the expected 3544316588U -160: file testGithub4764.sz1.svg gave hash 2364628953U not the expected 3611125861U -163: [00:25:02] The provided InitialSeed is not an MCS and will be ignored -160: file testGithub4764.sz2.svg gave hash 1490175526U not the expected 1936114454U -160: file testGithub4764.sz3.svg gave hash 1662881340U not the expected 2712214121U -186: iterative -160: file testGithub4764.sz1.png gave hash 517897906U not the expected 2179222277U -160: file testGithub4764.sz2.png gave hash 2568067924U not the expected 444262090U -148: .[00:25:02] Molecule does not have explicit Hs. Consider calling AddHs() -160: file testGithub4764.sz3.png gave hash 2910755141U not the expected 3567162200U -213: Randomness seeded to: 16401904 -213: =============================================================================== -213: All tests passed (273 assertions in 19 test cases) -213: -202/236 Test #213: testScaffoldNetwork .................... Passed 2.01 sec -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 -160: [00:25:03] 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 -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 -160: file test_github6112.svg gave hash 3865338574U not the expected 3278777629U -125: =============================================================================== -125: All tests passed (515 assertions in 10 test cases) -125: -203/236 Test #125: descriptorsTestCatch ................... Passed 6.27 sec -207: 375 -207: Enumeration has completed -195: ....................[00:25:03] Explicit valence for atom # 1 F, 2, is greater than permitted -195: [00:25:03] Explicit valence for atom # 6 F, 2, is greater than permitted -195: [00:25:03] Can't kekulize mol. Unkekulized atoms: 3 4 5 -207: [00:25:03] Tautomer enumeration stopped at 61 tautomers: canceled -195: .................[00:25:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -186: bulk -232: ....... -232: ---------------------------------------------------------------------- -232: Ran 11 tests in 1.954s -232: -232: OK -173: [00:25:03] Building the fingerprints may take some time. -160: file AtropManyChiralsEnhanced.svg gave hash 3443464321U not the expected 2256768013U -212: Enumeration has completed -204/236 Test #232: pySimDivPickers ........................ Passed 2.37 sec -212: [00:25:04] Tautomer enumeration stopped at 32 tautomers: canceled 150: processing 150: launch :0 150: launch :1 150: launch :2 150: launch :3 -146: processing -146: launch :0 -146: launch :1 -146: launch :2 -146: launch :3 -164: ........................................[00:25:04] The provided InitialSeed is not an MCS and will be ignored -164: [00:25:04] The provided InitialSeed is not an MCS and will be ignored -164: [00:25:04] The provided InitialSeed is not an MCS and will be ignored -164: .[00:25:04] The provided InitialSeed is not an MCS and will be ignored -164: [00:25:04] The provided InitialSeed is not an MCS and will be ignored -164: [00:25:04] The provided InitialSeed is not an MCS and will be ignored -164: .[00:25:04] The provided InitialSeed is not an MCS and will be ignored -164: [00:25:04] The provided InitialSeed is not an MCS and will be ignored -164: [00:25:04] The provided InitialSeed is not an MCS and will be ignored -164: .[00:25:04] The provided InitialSeed is not an MCS and will be ignored -164: [00:25:04] The provided InitialSeed is not an MCS and will be ignored -160: file testGithub_7739_1.svg gave hash 3358510977U not the expected 2615562225U -164: [00:25:04] The provided InitialSeed is not an MCS and will be ignored -117: =>start test GETAWAY custom -117: [00:25:04] test on : 365 molecules done -205/236 Test #117: testRDFcustom .......................... Passed 7.45 sec +164: ........................................[20:24:19] The provided InitialSeed is not an MCS and will be ignored +164: [20:24:19] The provided InitialSeed is not an MCS and will be ignored +164: [20:24:19] The provided InitialSeed is not an MCS and will be ignored +203/236 Test #229: pyMatCalc .............................. Passed 0.73 sec +164: .[20:24:20] The provided InitialSeed is not an MCS and will be ignored +164: [20:24:20] The provided InitialSeed is not an MCS and will be ignored +164: [20:24:20] The provided InitialSeed is not an MCS and will be ignored +148: [20:24:20] Molecule does not have explicit Hs. Consider calling AddHs() +164: .[20:24:20] The provided InitialSeed is not an MCS and will be ignored +213: Randomness seeded to: 258953545 +213: =============================================================================== +213: All tests passed (273 assertions in 19 test cases) +213: +164: [20:24:20] The provided InitialSeed is not an MCS and will be ignored +164: [20:24:20] The provided InitialSeed is not an MCS and will be ignored +204/236 Test #213: testScaffoldNetwork .................... Passed 2.35 sec +164: .[20:24:20] The provided InitialSeed is not an MCS and will be ignored +164: [20:24:20] The provided InitialSeed is not an MCS and will be ignored +164: [20:24:20] The provided InitialSeed is not an MCS and will be ignored 164: ................. 164: ---------------------------------------------------------------------- -164: Ran 60 tests in 6.166s +164: Ran 60 tests in 5.653s 164: 164: OK -160: file testGithub_7739_3.svg gave hash 176211825U not the expected 1037942338U -206/236 Test #164: pyFMCS ................................. Passed 6.61 sec -160: file testGithub_7739_4.svg gave hash 3309264286U not the expected 3549083171U -160: file testSmallReactionCanvas.svg gave hash 3859901121U not the expected 2238356155U -212: ..........[00:25:04] Explicit valence for atom # 1 N, 4, is greater than permitted -212: [00:25:04] Explicit valence for atom # 1 N, 4, is greater than permitted -212: [00:25:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -29: Checking against /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -212: [00:25:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -173: [00:25:04] -173: -173: **** -160: =============================================================================== -160: All tests passed (6857 assertions in 116 test cases) -160: -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# 0x000055A0B2D5556A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: 8# 0x000055A0B2D9FD78 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: 9# 0x000055A0B2DA0898 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: 10# 0x000055A0B2DA0D10 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: 11# 0x000055A0B2D722C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: 12# 0x000055A0B2D7262C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: 13# 0x000055A0B2D5478E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: 14# 0x00007F1851833CA8 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# 0x000055A0B2D547D1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: ---------- -173: **** -173: -173: [00:25:04] 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: [00:25:04] Explicit valence for atom # 4 C, 5, is greater than permitted -173: [00:25:04] 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 -207/236 Test #160: moldraw2DTestCatch ..................... Passed 7.08 sec -173: [00:25:04] Complex queries can be slow. -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: -29: All 191 tests passed -222: Randomness seeded to: 2103587352 -222: =============================================================================== -222: All tests passed (203 assertions in 1 test case) -222: -208/236 Test #222: testMolProcessing ...................... Passed 3.45 sec -173: [00:25:04] Complex queries can be slow. +207: [20:24:20] Tautomer enumeration stopped at 72 tautomers: canceled +207: Enumeration was canceled due to timeout (50 ms) +160: file AtropManyChiralsEnhanced.svg gave hash 3443464321U not the expected 2256768013U +205/236 Test #164: pyFMCS ................................. Passed 6.07 sec 126: Warning: Atom Count for residue GLU5A does not match expected count -207: CN=c1cc[nH]cn1 -207: CN=c1ccnc[nH]1 -207: CNc1ccncn1 -207: res: CNc1ccncn1 -207: CN=c1cccc[nH]1 -207: CNc1ccccn1 -207: res: CNc1ccccn1 126: Warning: Atom Count for residue ASN39A does not match expected count 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 -126: .[00:25:05] DEPRECATION WARNING: please use MorganGenerator -126: .[00:25:05] DEPRECATION WARNING: please use MorganGenerator -126: ..[00:25:05] DEPRECATION WARNING: please use AtomPairGenerator -126: [00:25:05] DEPRECATION WARNING: please use AtomPairGenerator -126: [00:25:05] DEPRECATION WARNING: please use AtomPairGenerator -126: [00:25:05] DEPRECATION WARNING: please use AtomPairGenerator -126: [00:25:05] DEPRECATION WARNING: please use AtomPairGenerator -126: [00:25:05] DEPRECATION WARNING: please use AtomPairGenerator -126: .[00:25:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [00:25:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: ...[00:25:05] DEPRECATION WARNING: please use MorganGenerator -126: [00:25:05] DEPRECATION WARNING: please use MorganGenerator -126: [00:25:05] DEPRECATION WARNING: please use MorganGenerator -126: [00:25:05] DEPRECATION WARNING: please use MorganGenerator -126: [00:25:05] DEPRECATION WARNING: please use MorganGenerator -126: [00:25:05] DEPRECATION WARNING: please use MorganGenerator -126: [00:25:05] DEPRECATION WARNING: please use MorganGenerator -126: [00:25:05] DEPRECATION WARNING: please use MorganGenerator -126: [00:25:05] DEPRECATION WARNING: please use MorganGenerator -126: [00:25:05] DEPRECATION WARNING: please use MorganGenerator -126: [00:25:05] DEPRECATION WARNING: please use MorganGenerator -126: [00:25:05] DEPRECATION WARNING: please use MorganGenerator -126: [00:25:05] DEPRECATION WARNING: please use MorganGenerator -126: [00:25:05] DEPRECATION WARNING: please use MorganGenerator -126: [00:25:05] DEPRECATION WARNING: please use MorganGenerator -126: [00:25:05] DEPRECATION WARNING: please use MorganGenerator -126: [00:25:05] DEPRECATION WARNING: please use MorganGenerator -126: [00:25:05] DEPRECATION WARNING: please use MorganGenerator -126: [00:25:05] DEPRECATION WARNING: please use MorganGenerator -126: [00:25:05] DEPRECATION WARNING: please use MorganGenerator -126: [00:25:05] DEPRECATION WARNING: please use MorganGenerator -126: [00:25:05] DEPRECATION WARNING: please use MorganGenerator -126: ....[00:25:05] DEPRECATION WARNING: please use AtomPairGenerator -126: [00:25:05] DEPRECATION WARNING: please use AtomPairGenerator -126: ....[00:25:05] DEPRECATION WARNING: please use AtomPairGenerator -126: [00:25:05] DEPRECATION WARNING: please use AtomPairGenerator -126: .[00:25:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [00:25:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [00:25:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [00:25:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [00:25:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: ..[00:25:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [00:25:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [00:25:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [00:25:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [00:25:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [00:25:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: .[00:25:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [00:25:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: .[20:24:20] DEPRECATION WARNING: please use MorganGenerator +126: .[20:24:20] DEPRECATION WARNING: please use MorganGenerator +126: ..[20:24:20] DEPRECATION WARNING: please use AtomPairGenerator +126: [20:24:20] DEPRECATION WARNING: please use AtomPairGenerator +126: [20:24:20] DEPRECATION WARNING: please use AtomPairGenerator +126: [20:24:20] DEPRECATION WARNING: please use AtomPairGenerator +126: [20:24:20] DEPRECATION WARNING: please use AtomPairGenerator +126: [20:24:20] DEPRECATION WARNING: please use AtomPairGenerator +126: .[20:24:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [20:24:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: ...[20:24:20] DEPRECATION WARNING: please use MorganGenerator +126: [20:24:20] DEPRECATION WARNING: please use MorganGenerator +126: [20:24:20] DEPRECATION WARNING: please use MorganGenerator +126: [20:24:20] DEPRECATION WARNING: please use MorganGenerator +126: [20:24:20] DEPRECATION WARNING: please use MorganGenerator +126: [20:24:20] DEPRECATION WARNING: please use MorganGenerator +126: [20:24:20] DEPRECATION WARNING: please use MorganGenerator +126: [20:24:20] DEPRECATION WARNING: please use MorganGenerator +126: [20:24:20] DEPRECATION WARNING: please use MorganGenerator +126: [20:24:20] DEPRECATION WARNING: please use MorganGenerator +126: [20:24:20] DEPRECATION WARNING: please use MorganGenerator +126: [20:24:20] DEPRECATION WARNING: please use MorganGenerator +126: [20:24:20] DEPRECATION WARNING: please use MorganGenerator +126: [20:24:20] DEPRECATION WARNING: please use MorganGenerator +126: [20:24:20] DEPRECATION WARNING: please use MorganGenerator +126: [20:24:20] DEPRECATION WARNING: please use MorganGenerator +126: [20:24:20] DEPRECATION WARNING: please use MorganGenerator +126: [20:24:20] DEPRECATION WARNING: please use MorganGenerator +126: [20:24:20] DEPRECATION WARNING: please use MorganGenerator +126: [20:24:20] DEPRECATION WARNING: please use MorganGenerator +126: [20:24:20] DEPRECATION WARNING: please use MorganGenerator +126: [20:24:20] DEPRECATION WARNING: please use MorganGenerator +126: ....[20:24:20] DEPRECATION WARNING: please use AtomPairGenerator +126: [20:24:20] DEPRECATION WARNING: please use AtomPairGenerator +126: ....[20:24:20] DEPRECATION WARNING: please use AtomPairGenerator +126: [20:24:20] DEPRECATION WARNING: please use AtomPairGenerator +126: .[20:24:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [20:24:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [20:24:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [20:24:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [20:24:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: ..[20:24:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [20:24:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [20:24:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [20:24:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [20:24:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [20:24:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: .[20:24:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [20:24:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: ... 126: ---------------------------------------------------------------------- -126: Ran 31 tests in 7.545s +126: Ran 31 tests in 6.583s 126: 126: OK 126: exactmw 78.046950192 @@ -32421,1059 +32366,124 @@ 126: CustomNumAtoms 6.0 126: exactmw 78.046950192 126: lipinskiHBA 0.0 -173: [00:25:05] Complex queries can be slow. -209/236 Test #126: pyMolDescriptors ....................... Passed 8.14 sec -183: [00:25:05] ------------------------------------- -183: [00:25:05] testing PatternHolder -29: -29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_dative.smi... -210/236 Test #207: molTautomerTest ........................ Passed 4.63 sec -173: [00:25:05] Complex queries can be slow. -183: [00:25:05] ------------------------------------- -183: [00:25:05] testing TautomerPatternHolder -173: [00:25:05] Complex queries can be slow. -173: [00:25:05] Complex queries can be slow. -183: [00:25:05] ------------------------------------- -183: [00:25:05] testSegFaultInHolder -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: '[00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1[00:25:05] dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1:[00:25:05] : -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] [00:25:05] ^ -183: [00:25:05] dsafsdf -183: [00:25:05] SMILES[00:25:05] Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: SMILES Parse Error: syntax error[00:25:05] ^ -183: while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position [00:25:05] syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf[00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'SMILES Parse Error: syntax error[00:25:05] while parsing: dsafsdf[00:25:05] dsafsdf[00:25:05] [00:25:05] SMILES Parse Error: syntax error while parsing: '[00:25:05] -183: SMILES Parse Error: syntax errordsafsdfSMILES Parse Error: -183: -183: [00:25:05] SMILES Parse Error: check for mistakes around position [00:25:05] SMILES Parse Error: syntax error1syntax errorSMILES Parse Error: check for mistakes around position SMILES Parse Error: 1:[00:25:05] syntax error while parsing: [00:25:05] dsafsdfSMILES Parse Error: while parsing: syntax error while parsing: :dsafsdfSMILES Parse Error: while parsing: -183: dsafsdf while parsing: [00:25:05] dsafsdfsyntax error -183: -183: dsafsdf -183: -183: -183: SMILES Parse Error: check for mistakes around position -183: while parsing: [00:25:05] SMILES Parse Error: check for mistakes around position [00:25:05] [00:25:05] SMILES Parse Error: check for mistakes around position dsafsdf11dsafsdf[00:25:05] -183: [00:25:05] -183: 1SMILES Parse Error: check for mistakes around position :1 -183: :[00:25:05] -183: dsafsdf[00:25:05] -183: ::dsafsdf -183: [00:25:05] [00:25:05] ^ -183: -183: -183: -183: dsafsdf[00:25:05] [00:25:05] ^ -183: SMILES Parse Error: check for mistakes around position [00:25:05] [00:25:05] dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position dsafsdf -183: [00:25:05] 1^[00:25:05] -183: -183: [00:25:05] :SMILESSMILES Parse Error: check for mistakes around position [00:25:05] 1: -183: -183: [00:25:05] [00:25:05] ^dsafsdf -183: ^ -183: [00:25:05] [00:25:05] ^[00:25:05] SMILES[00:25:05] Parse Error: dsafsdf -183: Failed parsing SMILES 'dsafsdf'1 for input: 'dsafsdf Parse Error: -183: -183: ' -183: [00:25:05] SMILESFailed parsing SMILES 'dsafsdf' Parse Error: Failed parsing SMILES 'dsafsdf'^[00:25:05] for input: 'dsafsdf -183: [00:25:05] 'SMILES for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: '[00:25:05] dsafsdf' -183: ^ -183: SMILES Parse Error: Failed parsing SMILES 'dsafsdf'SMILES Parse Error: for input: ' -183: [00:25:05] Failed parsing SMILES 'dsafsdf' Parse Error: Failed parsing SMILES 'dsafsdf'dsafsdf for input: ''dsafsdf -183: ' for input: ': -183: -183: dsafsdf'[00:25:05] SMILES -183: Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdfSMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1:'[00:25:05] dsafsdf -183: [00:25:05] [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: syntax error[00:25:05] while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: -183: SMILES Parse Error: [00:25:05] -183: [00:25:05] dsafsdf -183: [00:25:05] ^SMILES Parse Error: check for mistakes around position -183: syntax error while parsing: 1:SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: ' -183: dsafsdfdsafsdf' -183: -183: [00:25:05] SMILES Parse Error: check for mistakes around position [00:25:05] dsafsdf1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: '[00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: dsafsdf' -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] [00:25:05] [00:25:05] SMILESSMILES Parse Error: syntax error while parsing: dsafsdf[00:25:05] [00:25:05] [00:25:05] SMILES Parse Error: [00:25:05] Parse Error: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf[00:25:05] SMILES Parse Error: syntax errorsyntax errorSMILES Parse Error: ' while parsing: -183: syntax error while parsing: SMILES Parse Error: while parsing: syntax errordsafsdf -183: syntax errordsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: while parsing: [00:25:05] dsafsdfdsafsdfdsafsdf -183: [00:25:05] -183: -183: SMILES Parse Error: syntax error while parsing: [00:25:05] [00:25:05] [00:25:05] SMILES Parse Error: check for mistakes around position SMILES Parse Error: check for mistakes around position 1dsafsdf -183: ^[00:25:05] SMILES Parse Error: check for mistakes around position SMILES Parse Error: check for mistakes around position 1 while parsing: 1:: -183: -183: 1:[00:25:05] -183: [00:25:05] SMILES Parse Error: check for mistakes around position [00:25:05] :dsafsdf -183: -183: [00:25:05] -183: [00:25:05] 1SMILES Parse Error: check for mistakes around position :dsafsdfSMILES Parse Error: check for mistakes around position -183: 1dsafsdf[00:25:05] dsafsdf -183: [00:25:05] -183: -183: 1[00:25:05] : -183: -183: :[00:25:05] [00:25:05] dsafsdf^ -183: -183: dsafsdfSMILES -183: [00:25:05] [00:25:05] -183: [00:25:05] ^[00:25:05] -183: ^^ Parse Error: -183: ^ -183: Failed parsing SMILES 'dsafsdf'[00:25:05] SMILES[00:25:05] -183: [00:25:05] dsafsdf -183: for input: '[00:25:05] Parse Error: Failed parsing SMILES 'dsafsdf'[00:25:05] SMILES Parse Error: SMILES[00:25:05] dsafsdf -183: Failed parsing SMILES 'dsafsdf'[00:25:05] [00:25:05] for input: '^SMILESSMILESdsafsdf Parse Error: ' Parse Error: [00:25:05] Failed parsing SMILES 'dsafsdf'dsafsdf for input: 'dsafsdf for input: ' Parse Error: dsafsdf -183: Failed parsing SMILES 'dsafsdf'' for input: '' -183: Failed parsing SMILES 'dsafsdf' -183: dsafsdf''[00:25:05] -183: SMILES Parse Error: -183: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf for input: ' -183: ' -183: dsafsdf' -183: ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf[00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: SMILES Parse Error: [00:25:05] SMILES Parse Error: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: syntax error while parsing: dsafsdf -183: [00:25:05] [00:25:05] SMILES Parse Error: check for mistakes around position [00:25:05] SMILES Parse Error: check for mistakes around position syntax error1: -183: SMILES Parse Error: check for mistakes around position [00:25:05] while parsing: [00:25:05] SMILES Parse Error: syntax error while parsing: SMILES Parse Error: dsafsdfsyntax error -183: while parsing: dsafsdfdsafsdf[00:25:05] dsafsdf -183: 1: -183: -183: 1 -183: [00:25:05] [00:25:05] dsafsdf[00:25:05] [00:25:05] SMILES Parse Error: check for mistakes around position [00:25:05] :[00:25:05] SMILES Parse Error: check for mistakes around position -183: 1:SMILES Parse Error: check for mistakes around position 1 -183: ^SMILES Parse Error: [00:25:05] 1syntax error[00:25:05] while parsing: -183: dsafsdf -183: [00:25:05] :SMILES Parse Error: syntax error while parsing: dsafsdf^ -183: -183: -183: -183: [00:25:05] dsafsdf -183: : -183: SMILES Parse Error: check for mistakes around position [00:25:05] [00:25:05] [00:25:05] 1^[00:25:05] [00:25:05] [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf':[00:25:05] SMILESdsafsdfdsafsdf -183: [00:25:05] for input: '[00:25:05] -183: dsafsdf' Parse Error: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: ^ -183: -183: -183: SMILES Parse Error: [00:25:05] [00:25:05] [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: dsafsdf -183: [00:25:05] ^ -183: syntax error while parsing: -183: Failed parsing SMILES 'dsafsdf'[00:25:05] for input: 'dsafsdf' -183: SMILES Parse Error: syntax error while parsing: SMILES Parse Error: check for mistakes around position dsafsdf -183: 1[00:25:05] SMILES[00:25:05] Parse Error: Failed parsing SMILES 'dsafsdf'SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: '[00:25:05] [00:25:05] ^: -183: [00:25:05] dsafsdf -183: SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: dsafsdf -183: [00:25:05] [00:25:05] [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf[00:25:05] -183: SMILES Parse Error: [00:25:05] syntax error while parsing: dsafsdf -183: SMILESdsafsdf' -183: -183: [00:25:05] ^SMILES Parse Error: check for mistakes around position 1SMILES Parse Error: check for mistakes around position for input: ' -183: dsafsdf' -183: : -183: [00:25:05] [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: -183: 1:[00:25:05] [00:25:05] -183: SMILES Parse Error: syntax error while parsing: [00:25:05] [00:25:05] dsafsdf Parse Error: dsafsdf[00:25:05] dsafsdfSMILES^SMILES Parse Error: check for mistakes around position -183: 1 Parse Error: : -183: [00:25:05] Failed parsing SMILES 'dsafsdf'[00:25:05] dsafsdfSMILESdsafsdf -183: [00:25:05] ^ -183: -183: [00:25:05] ^ -183: -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: Parse Error: Failed parsing SMILES 'dsafsdf'Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf -183: -183: [00:25:05] [00:25:05] SMILES Parse Error: [00:25:05] ' -183: SMILES Parse Error: check for mistakes around position 1:[00:25:05] ^ for input: 'SMILESdsafsdf for input: ' -183: -183: ' -183: dsafsdf' -183: syntax error[00:25:05] [00:25:05] while parsing: dsafsdf[00:25:05] ^ -183: dsafsdf -183: [00:25:05] Parse Error: Failed parsing SMILES 'dsafsdf' for input: '[00:25:05] [00:25:05] SMILES^ -183: Parse Error: Failed parsing SMILES 'dsafsdf'SMILES for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: dsafsdf -183: ' -183: [00:25:05] SMILES Parse Error: check for mistakes around position Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: '[00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: '[00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1[00:25:05] dsafsdfdsafsdf' -183: ' -183: : -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: SMILES Parse Error: syntax error while parsing: SMILES Parse Error: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position syntax error[00:25:05] while parsing: [00:25:05] dsafsdf[00:25:05] [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: [00:25:05] -183: 1[00:25:05] : -183: [00:25:05] [00:25:05] dsafsdfSMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] [00:25:05] SMILES Parse Error: check for mistakes around position 1:SMILES Parse Error: syntax error while parsing: SMILES Parse Error: dsafsdfsyntax error while parsing: dsafsdf[00:25:05] -183: [00:25:05] SMILES Parse Error: check for mistakes around position [00:25:05] [00:25:05] SMILES Parse Error: syntax errorSMILES Parse Error: SMILES Parse Error: syntax error while parsing: dsafsdfsyntax error while parsing: -183: SMILES Parse Error: check for mistakes around position [00:25:05] [00:25:05] SMILES Parse Error: check for mistakes around position [00:25:05] -183: dsafsdf1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: SMILES Parse Error: check for mistakes around position 1: -183: SMILES Parse Error: while parsing: syntax errordsafsdf -183: while parsing: [00:25:05] SMILES Parse Error: check for mistakes around position 1SMILES Parse Error: syntax error while parsing: dsafsdf -183: -183: [00:25:05] [00:25:05] 1: -183: :[00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdfSMILES Parse Error: syntax errorsyntax error while parsing: dsafsdf -183: -183: SMILES Parse Error: -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1SMILES Parse Error: check for mistakes around position 1: -183: syntax error[00:25:05] [00:25:05] 1 while parsing: : -183: -183: [00:25:05] dsafsdf -183: :[00:25:05] [00:25:05] -183: [00:25:05] [00:25:05] [00:25:05] SMILES Parse Error: check for mistakes around position dsafsdf -183: SMILES Parse Error: check for mistakes around position [00:25:05] 1^: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: -183: [00:25:05] dsafsdf -183: [00:25:05] ^[00:25:05] while parsing: [00:25:05] dsafsdfdsafsdf -183: [00:25:05] ^ -183: 1: -183: dsafsdf[00:25:05] dsafsdf -183: dsafsdfdsafsdf -183: dsafsdf -183: -183: [00:25:05] SMILESSMILES Parse Error: check for mistakes around position -183: -183: [00:25:05] ^ -183: SMILES[00:25:05] -183: [00:25:05] [00:25:05] [00:25:05] 1^[00:25:05] :SMILES -183: ^[00:25:05] -183: ^ -183: Parse Error: [00:25:05] [00:25:05] SMILES Parse Error: [00:25:05] ^SMILESFailed parsing SMILES 'dsafsdf' Parse Error: for input: 'Failed parsing SMILES 'dsafsdf'[00:25:05] SMILES for input: 'SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: dsafsdf' -183: [00:25:05] SMILES Parse Error: Parse Error: Failed parsing SMILES 'dsafsdf'[00:25:05] for input: 'dsafsdf' -183: dsafsdf -183: 'Failed parsing SMILES 'dsafsdf' Parse Error: Parse Error: for input: 'dsafsdfSMILESFailed parsing SMILES 'dsafsdf' -183: '[00:25:05] -183: SMILES Parse Error: syntax error[00:25:05] for input: 'SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf Parse Error: ' -183: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: -183: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: dsafsdf' -183: [00:25:05] dsafsdf -183: [00:25:05] [00:25:05] SMILES Parse Error: check for mistakes around position ^ -183: dsafsdf -183: [00:25:05] 1: -183: [00:25:05] SMILES[00:25:05] ^ -183: dsafsdf -183: Parse Error: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'^ -183: -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:25:05] SMILES Parse Error: check for mistakes around position 1: -183: [00:25:05] dsafsdf -183: [00:25:05] ^ -183: [00:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:25:05] ------------------------------------- -183: [00:25:05] Results do not depend on numThreads -74: [00:25:05] Finished: testSmiCorrectness() -74: [00:25:05] ----------------------------------------- +206/236 Test #126: pyMolDescriptors ....................... Passed 7.13 sec +160: file testGithub_7739_1.svg gave hash 3358510977U not the expected 2615562225U +173: [20:24:20] Building the fingerprints may take some time. +160: file testGithub_7739_3.svg gave hash 176211825U not the expected 1037942338U +160: file testGithub_7739_4.svg gave hash 3309264286U not the expected 3549083171U +160: file testSmallReactionCanvas.svg gave hash 3859901121U not the expected 2238356155U +186: bulk +148: .[20:24:20] Molecule does not have explicit Hs. Consider calling AddHs() +160: =============================================================================== +160: All tests passed (6857 assertions in 116 test cases) +160: +207/236 Test #160: moldraw2DTestCatch ..................... Passed 6.93 sec +232: ....... +232: ---------------------------------------------------------------------- +232: Ran 11 tests in 1.210s +232: +232: OK +207: 375 +207: Enumeration has completed +208/236 Test #232: pySimDivPickers ........................ Passed 1.50 sec +207: [20:24:20] Tautomer enumeration stopped at 61 tautomers: canceled +173: [20:24:21] +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# 0x000055CC42F7456A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: 8# 0x000055CC42FBED78 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: 9# 0x000055CC42FBF898 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: 10# 0x000055CC42FBFD10 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: 11# 0x000055CC42F912C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: 12# 0x000055CC42F9162C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: 13# 0x000055CC42F7378E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: 14# 0x00007F5CA3E33CA8 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# 0x000055CC42F737D1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: ---------- +173: **** +173: +173: [20:24:21] 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: [20:24:21] Explicit valence for atom # 4 C, 5, is greater than permitted +173: [20:24:21] 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: [20:24:21] Complex queries can be slow. +173: [20:24:21] Complex queries can be slow. +146: processing +146: launch :0 +146: launch :1 +146: launch :2 +146: launch :3 +173: [20:24:21] Complex queries can be slow. +212: Enumeration has completed +212: [20:24:21] Tautomer enumeration stopped at 46 tautomers: canceled +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: +173: [20:24:21] Complex queries can be slow. +74: [20:24:21] Finished: testSmiCorrectness() +74: [20:24:21] ----------------------------------------- 74: -74: [00:25:05] +74: [20:24:21] 74: ----------------------------------------- -74: [00:25:06] Spurious data before the first property will be ignored -74: [00:25:06] Property will be truncated after the first blank line -74: [00:25:06] Property will be truncated after the first blank line -74: [00:25:06] Property will be truncated after the first blank line -173: [00:25:06] Complex queries can be slow. -212: ............[00:25:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -212: [00:25:06] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 1 ignored. -212: [00:25:06] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 1 ignored. -173: [00:25:06] Complex queries can be slow. -74: [00:25:06] Finished: testSDCorrectness() -74: [00:25:06] ----------------------------------------- +74: [20:24:21] Spurious data before the first property will be ignored +74: [20:24:21] Property will be truncated after the first blank line +74: [20:24:21] Property will be truncated after the first blank line +74: [20:24:21] Property will be truncated after the first blank line +173: [20:24:21] Complex queries can be slow. +212: ..........[20:24:21] Explicit valence for atom # 1 N, 4, is greater than permitted +212: [20:24:21] Explicit valence for atom # 1 N, 4, is greater than permitted +212: [20:24:21] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +212: [20:24:21] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +195: ....................[20:24:21] Explicit valence for atom # 1 F, 2, is greater than permitted +195: [20:24:21] Explicit valence for atom # 6 F, 2, is greater than permitted +195: [20:24:21] Can't kekulize mol. Unkekulized atoms: 3 4 5 +222: Randomness seeded to: 2264546823 +222: =============================================================================== +222: All tests passed (203 assertions in 1 test case) +222: +209/236 Test #222: testMolProcessing ...................... Passed 3.63 sec +195: .................[20:24:21] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +173: [20:24:21] Complex queries can be slow. +207: CN=c1cc[nH]cn1 +207: CN=c1ccnc[nH]1 +207: CNc1ccncn1 +207: res: CNc1ccncn1 +207: CN=c1cccc[nH]1 +207: CNc1ccccn1 +207: res: CNc1ccccn1 +173: [20:24:21] Complex queries can be slow. +74: [20:24:21] Finished: testSDCorrectness() +74: [20:24:21] ----------------------------------------- 74: -211/236 Test #74: testMultithreadedMolSupplier ........... Passed 9.72 sec -212: ........[00:25:06] Explicit valence for atom # 1 O, 3, is greater than permitted -173: [00:25:06] Complex queries can be slow. -186: bulk, no symmetry -212: .. -212: ---------------------------------------------------------------------- -212: Ran 38 tests in 5.032s -212: -212: OK -212: done -212/236 Test #212: pyMolStandardize ....................... Passed 5.59 sec -213/236 Test #199: pyTestThreads .......................... Passed 6.46 sec -173: [00:25:06] Complex queries can be slow. +210/236 Test #74: testMultithreadedMolSupplier ........... Passed 9.10 sec +173: [20:24:22] Complex queries can be slow. +211/236 Test #207: molTautomerTest ........................ Passed 4.56 sec +173: [20:24:22] Complex queries can be slow. 159: Done 159: ----------------- Test Github #781: Rendering single-atom molecules 159: Done 159: ----------------- Test 3 159: file test3_1.png gave hash 123800385U not the expected 675908852U 159: file test3_2.png gave hash 1032419673U not the expected 2452584093U -173: [00:25:06] Complex queries can be slow. +173: [20:24:22] Complex queries can be slow. 159: file test3_3.png gave hash 4020047355U not the expected 1907006999U 159: file test3_4.png gave hash 3725504342U not the expected 2305641511U 159: file test3_5.png gave hash 3317652686U not the expected 3842605920U @@ -33481,6 +32491,7 @@ 159: file test3_7.png gave hash 98439579U not the expected 469729412U 159: Done 159: ----------------- Test Github774: upside-down drawings +173: [20:24:22] Complex queries can be slow. 159: file test774_1.png gave hash 2947517748U not the expected 428322245U 159: file test774_2.png gave hash 3968995771U not the expected 4095288521U 159: Done @@ -33488,6 +32499,9 @@ 159: file test9_1.svg gave hash 923579170U not the expected 1484349178U 159: Done 159: ----------------- Test Github852: Lines used to wedge bonds are too thick +212: ............[20:24:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +212: [20:24:22] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 1 ignored. +212: [20:24:22] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 1 ignored. 159: file test852_1.png gave hash 1401513420U not the expected 271517011U 159: file test852_2.png gave hash 1268186246U not the expected 967452082U 159: ---------------- @@ -33517,8 +32531,8 @@ 159: ----------------- Testing drawing a grid of molecules 159: Done 159: ----------------- Testing drawMolecules +186: bulk, no symmetry 159: file test12_1.svg gave hash 76786371U not the expected 826649652U -186: [00:25:06] Relabelling existing label 159: Done 159: ----------------- Test JSON Configuration 159: Done @@ -33533,6 +32547,7 @@ 159: ----------------- Testing use of a black & white palette 159: Done 159: ----------------- Testing use of continuous highlighting with drawMolecules +212: ........[20:24:22] Explicit valence for atom # 1 O, 3, is greater than permitted 159: Done 159: ----------------- Test 17 - Testing maximum font size 159: Done @@ -33555,9 +32570,16 @@ 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 +212: .. +212: ---------------------------------------------------------------------- +212: Ran 38 tests in 4.989s +212: +212: OK +212: done 159: Done 159: ----------------- Testing annotation of 2D Drawing. 159: file test20_1.png gave hash 1197378089U not the expected 200877868U +212/236 Test #212: pyMolStandardize ....................... Passed 5.36 sec 159: file test20_2.png gave hash 717262667U not the expected 1651164846U 159: file test20_3.png gave hash 1844565424U not the expected 1463603076U 159: file test20_4.png gave hash 284908271U not the expected 1714613205U @@ -33571,7 +32593,6 @@ 159: ----------------- Test Github 3305 - change and scale line widths. 159: file testGithub3305_1.png gave hash 3066881557U not the expected 3303791649U 159: file testGithub3305_2.png gave hash 3473051322U not the expected 4003267433U -186: Best mapping 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 @@ -33589,8 +32610,22 @@ 159: Done 159: ----------------- Test AND queries 159: Done -214/236 Test #159: moldraw2DTest1 ......................... Passed 9.57 sec -215/236 Test #186: testRGroupDecomp ....................... Passed 8.35 sec +213/236 Test #159: moldraw2DTest1 ......................... Passed 9.39 sec +186: [20:24:23] Relabelling existing label +29: Checking against /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +186: Best mapping +29: All 191 tests passed +214/236 Test #186: testRGroupDecomp ....................... Passed 8.04 sec +183: [20:24:23] ------------------------------------- +183: [20:24:23] testing PatternHolder +29: +29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_dative.smi... +80: =============================================================================== +80: All tests passed (1596 assertions in 100 test cases) +80: +215/236 Test #80: fileParsersCatchTest ................... Passed 11.13 sec +183: [20:24:24] ------------------------------------- +183: [20:24:24] testing TautomerPatternHolder 177: VS001: PASSED 177: VS002: PASSED 177: VS003: PASSED @@ -33893,192 +32928,1033 @@ 177: VS300: PASSED 177: Check finished: 0 molecules failed. 177: Failed: -216/236 Test #177: pyCIPLabelsValidation .................. Passed 9.54 sec -80: =============================================================================== -80: All tests passed (1596 assertions in 100 test cases) -80: -217/236 Test #80: fileParsersCatchTest ................... Passed 11.79 sec -185: ......[00:25:08] -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# 0x00007F8AC8A5D1D5 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# 0x00007F8ACAE4862C 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# 0x00007F8AC89B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -185: 21# 0x00007F8AC89B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -185: 22# 0x00007F8AC89B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -185: 23# 0x00007F8AC89B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -185: 24# 0x00007F8AC89B7933 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# 0x00007F8ACAE453C6 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# 0x00007F8ACB78BCA8 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: [00:25:08] -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# 0x00007F8AC84E6800 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# 0x00007F8AC8A5D1D5 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# 0x00007F8ACAE4862C 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# 0x00007F8AC89B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -185: 22# 0x00007F8AC89B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -185: 23# 0x00007F8AC89B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -185: 24# 0x00007F8AC89B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -185: 25# 0x00007F8AC89B7933 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# 0x00007F8ACAE453C6 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# 0x00007F8ACB78BCA8 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: [00:25:08] ------------------------------------- -183: [00:25:08] Results do not depend on numThreads (all same) -183: [00:25:08] ------------------------------------- -183: [00:25:08] testTautomerQueries -183: [00:25:08] Pattern fingerprints for tautomersearch aren't tautomer fingerprints, ignoring... -183: [00:25:08] ------------------------------------- -183: [00:25:08] github3881 recursive smarts with rings -218/236 Test #183: substructLibraryTest ................... Passed 10.33 sec -152: .............[00:25:08] Molecule does not have explicit Hs. Consider calling AddHs() -152: [00:25:09] Molecule does not have explicit Hs. Consider calling AddHs() -152: [00:25:09] Molecule does not have explicit Hs. Consider calling AddHs() -152: [00:25:09] Molecule does not have explicit Hs. Consider calling AddHs() -152: [00:25:09] Molecule does not have explicit Hs. Consider calling AddHs() -152: [00:25:09] Molecule does not have explicit Hs. Consider calling AddHs() -152: [00:25:09] Molecule does not have explicit Hs. Consider calling AddHs() -152: [00:25:09] Molecule does not have explicit Hs. Consider calling AddHs() -152: [00:25:09] Molecule does not have explicit Hs. Consider calling AddHs() -152: [00:25:09] Molecule does not have explicit Hs. Consider calling AddHs() -152: [00:25:09] Molecule does not have explicit Hs. Consider calling AddHs() -170: Randomness seeded to: 1115072796 -170: [00:25:09] Timed out after 11 seconds. -29: Checking against /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -29: All 191 tests passed -29: -29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.smi... -195: ..[00:25:10] +183: [20:24:24] ------------------------------------- +183: [20:24:24] testSegFaultInHolder +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1:[20:24:24] SMILES Parse Error: syntax error while parsing: [20:24:24] +183: SMILES Parse Error: Failed parsing SMILES 'dsafsdf'[20:24:24] SMILES Parse Error: syntax error[20:24:24] for input: 'dsafsdf' +183: [20:24:24] dsafsdfSMILES Parse Error: +183: [20:24:24] ^ while parsing: dsafsdf +183: +183: [20:24:24] dsafsdfSMILES Parse Error: syntax error while parsing: dsafsdf +183: syntax error[20:24:24] SMILES Parse Error: check for mistakes around position 1[20:24:24] while parsing: dsafsdfSMILES Parse Error: [20:24:24] syntax error while parsing: dsafsdf +183: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: +183: [20:24:24] SMILES Parse Error: check for mistakes around position [20:24:24] SMILES Parse Error: [20:24:24] SMILES Parse Error: check for mistakes around position 11[20:24:24] SMILES Parse Error: check for mistakes around position [20:24:24] syntax errorSMILES Parse Error: 1syntax error: +183: while parsing: :dsafsdf +183: +183: : while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] [20:24:24] +183: [20:24:24] SMILES Parse Error: syntax error +183: ^ +183: [20:24:24] [20:24:24] dsafsdf[20:24:24] dsafsdf: +183: [20:24:24] +183: SMILES[20:24:24] [20:24:24] [20:24:24] SMILES Parse Error: [20:24:24] +183: SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] while parsing: syntax errordsafsdfSMILES Parse Error: [20:24:24] syntax error^ Parse Error: +183: SMILES Parse Error: check for mistakes around position [20:24:24] while parsing: dsafsdf^ +183: +183: dsafsdf while parsing: dsafsdfdsafsdf +183: dsafsdf +183: [20:24:24] +183: Failed parsing SMILES 'dsafsdf' for input: '1dsafsdf[20:24:24] [20:24:24] ^[20:24:24] [20:24:24] +183: ^ +183: : +183: +183: [20:24:24] [20:24:24] dsafsdfSMILES Parse Error: SMILES[20:24:24] Parse Error: +183: '[20:24:24] +183: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: '[20:24:24] dsafsdf'SMILES Parse Error: check for mistakes around position syntax errorSMILES[20:24:24] +183: [20:24:24] +183: Failed parsing SMILES 'dsafsdf'SMILES Parse Error: check for mistakes around position SMILES1 Parse Error: Failed parsing SMILES 'dsafsdf':SMILES Parse Error: check for mistakes around position +183: [20:24:24] ^[20:24:24] +183: dsafsdf +183: while parsing: 1: Parse Error: 1Failed parsing SMILES 'dsafsdf' for input: ': +183: [20:24:24] for input: '^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'dsafsdfdsafsdf[20:24:24] [20:24:24] +183: [20:24:24] [20:24:24] dsafsdf' +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'SMILES Parse Error: +183: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdfdsafsdf +183: ' +183: [20:24:24] ^[20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] [20:24:24] +183: for input: ' +183: +183: [20:24:24] ^ +183: dsafsdf' +183: SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf[20:24:24] dsafsdfSMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'SMILES Parse Error: ^[20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] +183: SMILES Parse Error: syntax error[20:24:24] +183: SMILES Parse Error: check for mistakes around position SMILES Parse Error: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] +183: dsafsdf +183: SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES[20:24:24] Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'syntax errordsafsdf while parsing: while parsing: [20:24:24] +183: SMILES Parse Error: [20:24:24] ' +183: SMILES Parse Error: check for mistakes around position dsafsdfsyntax error +183: while parsing: dsafsdf +183: 1[20:24:24] ^dsafsdf +183: 1[20:24:24] SMILES Parse Error: check for mistakes around position SMILES Parse Error: check for mistakes around position [20:24:24] :^[20:24:24] [20:24:24] dsafsdf[20:24:24] +183: +183: 1[20:24:24] SMILES Parse Error: check for mistakes around position syntax errorSMILES Parse Error: while parsing: syntax error[20:24:24] SMILES Parse Error: check for mistakes around position 1 while parsing: SMILES Parse Error: : +183: 1: +183: 1:[20:24:24] [20:24:24] :SMILES +183: +183: [20:24:24] SMILES[20:24:24] [20:24:24] dsafsdfdsafsdf +183: dsafsdf[20:24:24] +183: Parse Error: +183: [20:24:24] ^ +183: ^ +183: syntax errordsafsdf Parse Error: +183: Failed parsing SMILES 'dsafsdf': for input: 'dsafsdf[20:24:24] +183: Failed parsing SMILES 'dsafsdf'SMILES +183: for input: ' while parsing: [20:24:24] dsafsdf +183: '[20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: ^[20:24:24] Parse Error: +183: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] dsafsdfSMILES +183: [20:24:24] ^ +183: SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] [20:24:24] SMILESdsafsdf +183: [20:24:24] +183: SMILES Parse Error: check for mistakes around position 1: +183: ^[20:24:24] +183: [20:24:24] [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' Parse Error: for input: '[20:24:24] Parse Error: [20:24:24] 'SMILES Parse Error: check for mistakes around position Failed parsing SMILES 'dsafsdf' for input: 'dsafsdfFailed parsing SMILES 'dsafsdf'SMILES Parse Error: for input: 'dsafsdfSMILES' Parse Error: Failed parsing SMILES 'dsafsdf' for input: '[20:24:24] dsafsdf +183: ' +183: 1[20:24:24] dsafsdf +183: [20:24:24] [20:24:24] dsafsdf[20:24:24] [20:24:24] ^ +183: +183: [20:24:24] +183: [20:24:24] SMILES Parse Error: syntax error:^dsafsdf +183: dsafsdf +183: [20:24:24] ' +183: [20:24:24] SMILES Parse Error: +183: ^[20:24:24] [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] +183: dsafsdfsyntax error +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: syntax error[20:24:24] +183: SMILES Parse Error: [20:24:24] ' +183: SMILES Parse Error: syntax errorFailed parsing SMILES 'dsafsdf' for input: ' while parsing: [20:24:24] SMILES Parse Error: check for mistakes around position while parsing: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: dsafsdf[20:24:24] while parsing: dsafsdfdsafsdfdsafsdf +183: dsafsdf +183: [20:24:24] ^ +183: ^ +183: SMILES[20:24:24] 1:[20:24:24] [20:24:24] +183: SMILES +183: SMILES Parse Error: [20:24:24] Parse Error: SMILES Parse Error: check for mistakes around position 1: Parse Error: SMILES Parse Error: '[20:24:24] dsafsdfFailed parsing SMILES 'dsafsdf'[20:24:24] [20:24:24] SMILES Parse Error: syntax error +183: [20:24:24] ' +183: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: ' for input: 'dsafsdfdsafsdf' +183: ' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: +183: +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf'Failed parsing SMILES 'dsafsdf' for input: 'dsafsdfdsafsdf' +183: [20:24:24] SMILES Parse Error: [20:24:24] [20:24:24] +183: ^[20:24:24] while parsing: +183: dsafsdfsyntax error[20:24:24] while parsing: [20:24:24] SMILES Parse Error: check for mistakes around position +183: 1: +183: [20:24:24] [20:24:24] SMILES Parse Error: syntax errorsyntax error while parsing: dsafsdfSMILES +183: Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf +183: for input: '[20:24:24] syntax errorSMILES Parse Error: check for mistakes around position while parsing: SMILES Parse Error: dsafsdf +183: [20:24:24] syntax errorSMILES Parse Error: check for mistakes around position 1[20:24:24] [20:24:24] while parsing: ^dsafsdf +183: :[20:24:24] 1dsafsdfSMILES Parse Error: check for mistakes around position +183: [20:24:24] SMILES Parse Error: SMILES Parse Error: check for mistakes around position SMILES Parse Error: :[20:24:24] ' +183: +183: SMILES Parse Error: [20:24:24] SMILES Parse Error: check for mistakes around position dsafsdfsyntax error +183: while parsing: 1syntax error while parsing: +183: [20:24:24] dsafsdf +183: dsafsdf^ +183: +183: : +183: [20:24:24] dsafsdf[20:24:24] dsafsdf' +183: [20:24:24] ^1SMILES Parse Error: check for mistakes around position 1syntax error while parsing: dsafsdf +183: while parsing: [20:24:24] [20:24:24] [20:24:24] SMILES Parse Error: check for mistakes around position [20:24:24] ^[20:24:24] SMILES Parse Error: check for mistakes around position +183: +183: [20:24:24] SMILES Parse Error: +183: :1SMILES Parse Error: check for mistakes around position :[20:24:24] 1SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf[20:24:24] ^[20:24:24] +183: SMILES Parse Error: Failed parsing SMILES 'dsafsdf': for input: 'dsafsdf[20:24:24] SMILES +183: Parse Error: 1 +183: SMILES Parse Error: :syntax errorsyntax error +183: 1'[20:24:24] dsafsdf +183: [20:24:24] ^ +183: while parsing: [20:24:24] dsafsdf +183: dsafsdf[20:24:24] [20:24:24] +183: Failed parsing SMILES 'dsafsdf' while parsing: SMILES +183: +183: dsafsdf[20:24:24] +183: dsafsdfdsafsdf +183: +183: +183: [20:24:24] [20:24:24] :SMILES[20:24:24] [20:24:24] [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: check for mistakes around position Parse Error: :[20:24:24] dsafsdfSMILES +183: Parse Error: +183: Parse Error: Failed parsing SMILES 'dsafsdf'[20:24:24] for input: 'Failed parsing SMILES 'dsafsdf'SMILES[20:24:24] for input: 'dsafsdfSMILES Parse Error: check for mistakes around position +183: 1: +183: [20:24:24] dsafsdfdsafsdf +183: 1dsafsdf: +183: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdfdsafsdf' +183: Parse Error: Failed parsing SMILES 'dsafsdf'[20:24:24] dsafsdf for input: ''dsafsdf[20:24:24] ' +183: ^ +183: [20:24:24] for input: ''[20:24:24] +183: SMILESdsafsdf Parse Error: +183: ^ +183: Failed parsing SMILES 'dsafsdf'[20:24:24] for input: 'dsafsdf' +183: [20:24:24] ^ +183: +183: ' +183: [20:24:24] SMILES Parse Error: +183: [20:24:24] [20:24:24] ^ +183: [20:24:24] [20:24:24] Failed parsing SMILES 'dsafsdf' for input: ' +183: +183: [20:24:24] dsafsdf +183: [20:24:24] dsafsdfdsafsdf' +183: ' +183: ^ +183: SMILES Parse Error: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf'syntax error while parsing: SMILES Parse Error: syntax error while parsing: dsafsdf[20:24:24] [20:24:24] SMILES Parse Error: [20:24:24] [20:24:24] SMILESSMILES Parse Error: ^ for input: ' +183: dsafsdf' +183: dsafsdfSMILESdsafsdf^ Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf +183: [20:24:24] +183: SMILES Parse Error: Parse Error: Failed parsing SMILES 'dsafsdf'Failed parsing SMILES 'dsafsdf'syntax error while parsing: syntax error +183: while parsing: for input: '[20:24:24] 'SMILES Parse Error: check for mistakes around position +183: 1: +183: +183: for input: 'dsafsdfdsafsdf[20:24:24] ' +183: SMILES Parse Error: check for mistakes around position 1: +183: 'dsafsdf +183: +183: [20:24:24] [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf'dsafsdf[20:24:24] +183: [20:24:24] dsafsdfSMILES Parse Error: check for mistakes around position 1[20:24:24] : +183: [20:24:24] SMILES Parse Error: check for mistakes around position for input: '1:[20:24:24] +183: SMILES Parse Error: check for mistakes around position dsafsdf +183: +183: [20:24:24] dsafsdf1[20:24:24] ^ +183: +183: [20:24:24] ^ +183: [20:24:24] dsafsdfSMILES Parse Error: +183: [20:24:24] ^ +183: dsafsdf' +183: : +183: [20:24:24] SMILES[20:24:24] ^[20:24:24] dsafsdf Parse Error: Failed parsing SMILES 'dsafsdf'Failed parsing SMILES 'dsafsdf' for input: ' +183: dsafsdf' +183: +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf for input: '[20:24:24] dsafsdf' +183: SMILES Parse Error: ' +183: [20:24:24] ^ +183: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf[20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1[20:24:24] [20:24:24] SMILES Parse Error: syntax error:SMILES Parse Error: syntax error[20:24:24] SMILES Parse Error: [20:24:24] dsafsdfsyntax error while parsing: while parsing: dsafsdf +183: while parsing: +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: +183: [20:24:24] [20:24:24] dsafsdf[20:24:24] [20:24:24] ^ +183: SMILES Parse Error: dsafsdfSMILES Parse Error: syntax error while parsing: dsafsdf[20:24:24] +183: dsafsdf +183: [20:24:24] ^ +183: syntax error[20:24:24] [20:24:24] SMILES Parse Error: [20:24:24] SMILES Parse Error: while parsing: dsafsdfSMILES Parse Error: [20:24:24] Failed parsing SMILES 'dsafsdf'Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf +183: +183: [20:24:24] [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] +183: SMILES Parse Error: syntax error while parsing: [20:24:24] dsafsdfSMILES Parse Error: check for mistakes around position 1SMILES Parse Error: check for mistakes around position ' +183: for input: ' +183: [20:24:24] [20:24:24] SMILES Parse Error: [20:24:24] syntax error while parsing: dsafsdfSMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] 1SMILES Parse Error: check for mistakes around position syntax errordsafsdf[20:24:24] [20:24:24] ^1dsafsdf:: +183: [20:24:24] [20:24:24] SMILES Parse Error: check for mistakes around position SMILES Parse Error: +183: ' +183: +183: :[20:24:24] 1 while parsing: SMILES Parse Error: [20:24:24] +183: SMILES Parse Error: +183: syntax error[20:24:24] while parsing: dsafsdf +183: [20:24:24] [20:24:24] ^SMILES Parse Error: +183: syntax errorsyntax error[20:24:24] while parsing: [20:24:24] dsafsdfdsafsdf +183: :[20:24:24] SMILES Parse Error: SMILES Parse Error: check for mistakes around position SMILES +183: +183: [20:24:24] while parsing: dsafsdf1dsafsdf[20:24:24] Parse Error: SMILES Parse Error: check for mistakes around position :syntax errordsafsdfSMILES Parse Error: check for mistakes around position +183: +183: 1syntax error +183: [20:24:24] [20:24:24] while parsing: dsafsdf +183: Failed parsing SMILES 'dsafsdf' +183: dsafsdf[20:24:24] +183: ^: for input: ' +183: [20:24:24] [20:24:24] while parsing: dsafsdf[20:24:24] +183: ^dsafsdf[20:24:24] ^SMILESSMILES Parse Error: Parse Error: syntax errorFailed parsing SMILES 'dsafsdf'dsafsdf while parsing: +183: [20:24:24] 'dsafsdf[20:24:24] [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: +183: SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: +183: ^ +183: [20:24:24] for input: 'SMILES1[20:24:24] +183: : Parse Error: +183: dsafsdf[20:24:24] [20:24:24] [20:24:24] SMILESSMILES Parse Error: check for mistakes around position Parse Error: [20:24:24] +183: SMILES Parse Error: [20:24:24] Failed parsing SMILES 'dsafsdf''SMILES Parse Error: check for mistakes around position +183: dsafsdf +183: Failed parsing SMILES 'dsafsdf'[20:24:24] for input: 'dsafsdf'[20:24:24] +183: [20:24:24] dsafsdfSMILES +183: for input: 'SMILES Parse Error: check for mistakes around position dsafsdf Parse Error: [20:24:24] [20:24:24] ^ +183: Failed parsing SMILES 'dsafsdf'^Failed parsing SMILES 'dsafsdf'1: +183: [20:24:24] 'dsafsdf +183: [20:24:24] ^1 +183: :1 +183: for input: 'dsafsdf for input: '' +183: :SMILES[20:24:24] +183: SMILES +183: [20:24:24] [20:24:24] [20:24:24] Parse Error: [20:24:24] [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' +183: dsafsdf +183: SMILES Parse Error: for input: 'syntax error while parsing: dsafsdf[20:24:24] Parse Error: dsafsdf[20:24:24] +183: SMILES Parse Error: syntax error[20:24:24] while parsing: dsafsdf +183: dsafsdfdsafsdf' +183: Failed parsing SMILES 'dsafsdf' for input: 'SMILES Parse Error: dsafsdf' +183: +183: syntax errorSMILES while parsing: dsafsdf Parse Error: +183: [20:24:24] [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdfSMILES Parse Error: +183: SMILES Parse Error: check for mistakes around position 1[20:24:24] Failed parsing SMILES 'dsafsdf':SMILES Parse Error: check for mistakes around position [20:24:24] 1: +183: SMILES Parse Error: +183: [20:24:24] SMILES Parse Error: syntax error[20:24:24] [20:24:24] 'dsafsdf +183: [20:24:24] ^syntax error +183: while parsing: dsafsdf for input: ' +183: dsafsdf'[20:24:24] SMILES Parse Error: [20:24:24] dsafsdf while parsing: +183: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position +183: [20:24:24] [20:24:24] ^ +183: +183: 1[20:24:24] SMILES Parse Error: check for mistakes around position 1SMILES Parse Error: check for mistakes around position [20:24:24] 1:dsafsdf +183: Failed parsing SMILES 'dsafsdf'[20:24:24] [20:24:24] :SMILES Parse Error: syntax error while parsing: dsafsdf +183: SMILES Parse Error: syntax error while parsing: : +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'[20:24:24] [20:24:24] syntax error +183: while parsing: +183: dsafsdfsyntax errorSMILES for input: 'dsafsdf[20:24:24] ' +183: while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'dsafsdf +183: +183: SMILES Parse Error: check for mistakes around position 1 +183: [20:24:24] SMILES Parse Error: check for mistakes around position [20:24:24] [20:24:24] SMILES Parse Error: check for mistakes around position 1: Parse Error: +183: [20:24:24] dsafsdf1:: +183: Failed parsing SMILES 'dsafsdf' +183: SMILES Parse Error: [20:24:24] [20:24:24] dsafsdf +183: ^[20:24:24] ^ for input: ' +183: +183: +183: [20:24:24] [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf'[20:24:24] SMILES Parse Error: check for mistakes around position 1[20:24:24] dsafsdf[20:24:24] dsafsdfdsafsdf[20:24:24] 'SMILES Parse Error: SMILESSMILES Parse Error: Failed parsing SMILES 'dsafsdf' +183: for input: 'dsafsdf for input: ' +183: syntax error[20:24:24] +183: syntax errorSMILES Parse Error: syntax error while parsing: dsafsdf +183: +183: [20:24:24] dsafsdfdsafsdf' +183: [20:24:24] +183: : while parsing: +183: dsafsdf[20:24:24] +183: dsafsdf[20:24:24] SMILES Parse Error: check for mistakes around position 1 +183: : +183: [20:24:24] SMILES Parse Error: '[20:24:24] [20:24:24] +183: SMILES Parse Error: check for mistakes around position [20:24:24] 1:SMILES Parse Error: [20:24:24] syntax error[20:24:24] dsafsdfsyntax error while parsing: +183: ^ while parsing: SMILES Parse Error: [20:24:24] SMILES Parse Error: check for mistakes around position dsafsdf while parsing: [20:24:24] ^ +183: 1: +183: [20:24:24] [20:24:24] +183: SMILESdsafsdf +183: [20:24:24] dsafsdf^syntax error +183: [20:24:24] +183: SMILES Parse Error: check for mistakes around position ^[20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' +183: while parsing: 1dsafsdf[20:24:24] [20:24:24] SMILES Parse Error: check for mistakes around position +183: +183: +183: [20:24:24] dsafsdf[20:24:24] dsafsdf +183: [20:24:24] : Parse Error: for input: 'dsafsdf'^ +183: SMILES Parse Error: +183: 1:SMILES[20:24:24] +183: SMILES Parse Error: syntax error^ while parsing: [20:24:24] +183: +183: dsafsdf +183: [20:24:24] [20:24:24] Parse Error: [20:24:24] Parse Error: ^[20:24:24] +183: syntax error +183: SMILESFailed parsing SMILES 'dsafsdf' +183: [20:24:24] [20:24:24] [20:24:24] dsafsdf[20:24:24] [20:24:24] ^ +183: SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf[20:24:24] +183: +183: dsafsdf +183: [20:24:24] ^ +183: SMILES Parse Error: check for mistakes around position Failed parsing SMILES 'dsafsdf'1 for input: 'SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'[20:24:24] [20:24:24] [20:24:24] ^SMILES[20:24:24] SMILES^ +183: ^SMILES Parse Error: for input: 'syntax errordsafsdf while parsing: : Parse Error: +183: +183: +183: dsafsdf[20:24:24] [20:24:24] SMILES Parse Error: while parsing: [20:24:24] dsafsdf +183: dsafsdfFailed parsing SMILES 'dsafsdf'SMILES Parse Error: Parse Error: syntax errorSMILES' Parse Error: Failed parsing SMILES 'dsafsdf'[20:24:24] for input: '[20:24:24] SMILES Parse Error: dsafsdf' +183: dsafsdf Parse Error: [20:24:24] Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'SMILES Parse Error: check for mistakes around position 1[20:24:24] Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf +183: ' while parsing: +183: dsafsdf +183: SMILES Parse Error: [20:24:24] [20:24:24] 'SMILES Parse Error: syntax error +183: +183: while parsing: +183: dsafsdf +183: [20:24:24] SMILES Parse Error: [20:24:24] syntax error[20:24:24] SMILES Parse Error: check for mistakes around position SMILES Parse Error: :[20:24:24] [20:24:24] SMILES Parse Error: check for mistakes around position SMILES^syntax errorFailed parsing SMILES 'dsafsdf' while parsing: +183: [20:24:24] 1:[20:24:24] SMILES Parse Error: check for mistakes around position SMILES for input: 'dsafsdf[20:24:24] Parse Error: dsafsdf +183: SMILES Parse Error: dsafsdf while parsing: +183: ' +183: +183: SMILES Parse Error: [20:24:24] +183: syntax error +183: 1syntax errordsafsdfSMILES Parse Error: [20:24:24] syntax error[20:24:24] dsafsdf +183: ^ +183: while parsing: :syntax error +183: [20:24:24] [20:24:24] SMILES while parsing: [20:24:24] dsafsdfdsafsdf +183: +183: +183: Failed parsing SMILES 'dsafsdf'[20:24:24] ^ +183: for input: 'dsafsdf +183: '[20:24:24] SMILESSMILES Parse Error: check for mistakes around position while parsing: while parsing: 1 Parse Error: [20:24:24] ^[20:24:24] Parse Error: SMILES Parse Error: check for mistakes around position +183: [20:24:24] [20:24:24] 1dsafsdf: +183: +183: +183: dsafsdf[20:24:24] +183: dsafsdfdsafsdfFailed parsing SMILES 'dsafsdf'1: Parse Error: dsafsdf[20:24:24] +183: +183: [20:24:24] +183: : for input: 'dsafsdf +183: 'SMILES Parse Error: check for mistakes around position 1 +183: [20:24:24] Failed parsing SMILES 'dsafsdf' for input: 'SMILES:SMILES Parse Error: check for mistakes around position [20:24:24] 1:SMILES Parse Error: check for mistakes around position 1dsafsdf^[20:24:24] +183: [20:24:24] [20:24:24] ^ +183: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] dsafsdfFailed parsing SMILES 'dsafsdf'SMILES +183: Parse Error: +183: [20:24:24] [20:24:24] ^ +183: for input: 'SMILES Parse Error: check for mistakes around position Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf +183: 'dsafsdf +183: ' +183: [20:24:24] [20:24:24] for input: '[20:24:24] dsafsdf'dsafsdf +183: 1:: +183: Failed parsing SMILES 'dsafsdf' Parse Error: SMILESFailed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] dsafsdf^ +183: +183: [20:24:24] [20:24:24] dsafsdf +183: [20:24:24] +183: ^ +183: for input: '[20:24:24] [20:24:24] +183: SMILES Parse Error: Failed parsing SMILES 'dsafsdf'[20:24:24] dsafsdf +183: [20:24:24] ^ +183: dsafsdf Parse Error: '[20:24:24] for input: ' +183: dsafsdf'SMILES[20:24:24] Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdfSMILES Parse Error: Failed parsing SMILES 'dsafsdf'SMILES for input: 'SMILES'Failed parsing SMILES 'dsafsdf'' Parse Error: +183: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' Parse Error: +183: Failed parsing SMILES 'dsafsdf'SMILES +183: Failed parsing SMILES 'dsafsdf' for input: ' +183: dsafsdf' Parse Error: Failed parsing SMILES 'dsafsdf' for input: ' for input: '[20:24:24] dsafsdf' +183: for input: 'dsafsdf^dsafsdf' +183: +183: dsafsdf' +183: ' +183: +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdfdsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: ' +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +216/236 Test #177: pyCIPLabelsValidation .................. Passed 9.11 sec +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [20:24:24] SMILES Parse Error: check for mistakes around position 1: +183: [20:24:24] dsafsdf +183: [20:24:24] ^ +183: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [20:24:24] ------------------------------------- +183: [20:24:24] Results do not depend on numThreads +217/236 Test #199: pyTestThreads .......................... Passed 7.38 sec +152: .............[20:24:25] Molecule does not have explicit Hs. Consider calling AddHs() +152: [20:24:25] Molecule does not have explicit Hs. Consider calling AddHs() +152: [20:24:25] Molecule does not have explicit Hs. Consider calling AddHs() +152: [20:24:25] Molecule does not have explicit Hs. Consider calling AddHs() +152: [20:24:25] Molecule does not have explicit Hs. Consider calling AddHs() +152: [20:24:25] Molecule does not have explicit Hs. Consider calling AddHs() +152: [20:24:25] Molecule does not have explicit Hs. Consider calling AddHs() +152: [20:24:25] Molecule does not have explicit Hs. Consider calling AddHs() +152: [20:24:25] Molecule does not have explicit Hs. Consider calling AddHs() +152: [20:24:25] Molecule does not have explicit Hs. Consider calling AddHs() +152: [20:24:25] Molecule does not have explicit Hs. Consider calling AddHs() +170: Randomness seeded to: 433041920 +170: [20:24:25] Timed out after 11 seconds. +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 13.13 sec +195: ..[20:24:27] 195: 195: **** 195: Pre-condition Violation @@ -34092,7 +33968,7 @@ 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# 0x00007F916DC0662C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 5# 0x00007FB3B89D062C 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 @@ -34103,17 +33979,17 @@ 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# 0x00007F916B3B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 17# 0x00007F916B3B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 18# 0x00007F916B3B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 19# 0x00007F916B3B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 20# 0x00007F916B3B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 16# 0x00007FB3B61B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 17# 0x00007FB3B61B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 18# 0x00007FB3B61B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 19# 0x00007FB3B61B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 20# 0x00007FB3B61B7933 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# 0x00007F916DC033C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 26# 0x00007FB3B89CD3C6 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 @@ -34145,13 +34021,13 @@ 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# 0x00007F916E3E0CA8 in /lib/x86_64-linux-gnu/libc.so.6 +195: 58# 0x00007FB3B91AACA8 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: [00:25:10] +195: [20:24:27] 195: 195: **** 195: Pre-condition Violation @@ -34165,7 +34041,7 @@ 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# 0x00007F916DC0662C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 5# 0x00007FB3B89D062C 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 @@ -34176,17 +34052,17 @@ 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# 0x00007F916B3B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 17# 0x00007F916B3B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 18# 0x00007F916B3B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 19# 0x00007F916B3B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 20# 0x00007F916B3B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 16# 0x00007FB3B61B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 17# 0x00007FB3B61B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 18# 0x00007FB3B61B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 19# 0x00007FB3B61B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 20# 0x00007FB3B61B7933 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# 0x00007F916DC033C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 26# 0x00007FB3B89CD3C6 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 @@ -34218,13 +34094,13 @@ 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# 0x00007F916E3E0CA8 in /lib/x86_64-linux-gnu/libc.so.6 +195: 58# 0x00007FB3B91AACA8 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: [00:25:10] +195: [20:24:27] 195: 195: **** 195: Pre-condition Violation @@ -34238,7 +34114,7 @@ 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# 0x00007F916DC0662C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 5# 0x00007FB3B89D062C 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 @@ -34249,17 +34125,17 @@ 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# 0x00007F916B3B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 17# 0x00007F916B3B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 18# 0x00007F916B3B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 19# 0x00007F916B3B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 20# 0x00007F916B3B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 16# 0x00007FB3B61B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 17# 0x00007FB3B61B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 18# 0x00007FB3B61B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 19# 0x00007FB3B61B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 20# 0x00007FB3B61B7933 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# 0x00007F916DC033C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 26# 0x00007FB3B89CD3C6 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 @@ -34291,13 +34167,13 @@ 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# 0x00007F916E3E0CA8 in /lib/x86_64-linux-gnu/libc.so.6 +195: 58# 0x00007FB3B91AACA8 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: [00:25:10] +195: [20:24:27] 195: 195: **** 195: Pre-condition Violation @@ -34311,7 +34187,7 @@ 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# 0x00007F916DC0662C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 5# 0x00007FB3B89D062C 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 @@ -34322,17 +34198,17 @@ 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# 0x00007F916B3B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 17# 0x00007F916B3B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 18# 0x00007F916B3B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 19# 0x00007F916B3B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 20# 0x00007F916B3B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 16# 0x00007FB3B61B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 17# 0x00007FB3B61B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 18# 0x00007FB3B61B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 19# 0x00007FB3B61B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 20# 0x00007FB3B61B7933 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# 0x00007F916DC033C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 26# 0x00007FB3B89CD3C6 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 @@ -34364,13 +34240,13 @@ 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# 0x00007F916E3E0CA8 in /lib/x86_64-linux-gnu/libc.so.6 +195: 58# 0x00007FB3B91AACA8 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: [00:25:10] +195: [20:24:27] 195: 195: **** 195: Pre-condition Violation @@ -34384,7 +34260,7 @@ 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# 0x00007F916DC0662C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 5# 0x00007FB3B89D062C 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 @@ -34395,17 +34271,17 @@ 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# 0x00007F916B3B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 17# 0x00007F916B3B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 18# 0x00007F916B3B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 19# 0x00007F916B3B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 20# 0x00007F916B3B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 16# 0x00007FB3B61B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 17# 0x00007FB3B61B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 18# 0x00007FB3B61B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 19# 0x00007FB3B61B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 20# 0x00007FB3B61B7933 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# 0x00007F916DC033C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 26# 0x00007FB3B89CD3C6 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 @@ -34437,21 +34313,15 @@ 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# 0x00007F916E3E0CA8 in /lib/x86_64-linux-gnu/libc.so.6 +195: 58# 0x00007FB3B91AACA8 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: .....[00:25:10] +195: .....[20:24:27] 195: 195: **** -95: 0,0 0 -95: 0,1 0 -95: 1,0 0 -95: 1,1 0 -95: 2,0 0 -95: 2,1 0 195: Range Error 195: atomIdx1 195: Violation occurred on line 498 in file ./Code/GraphMol/RWMol.cpp @@ -34463,7 +34333,7 @@ 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# 0x00007F916DC0662C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 5# 0x00007FB3B89D062C 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 @@ -34474,17 +34344,17 @@ 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# 0x00007F916B3B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 17# 0x00007F916B3B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 18# 0x00007F916B3B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 19# 0x00007F916B3B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 20# 0x00007F916B3B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 16# 0x00007FB3B61B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 17# 0x00007FB3B61B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 18# 0x00007FB3B61B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 19# 0x00007FB3B61B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 20# 0x00007FB3B61B7933 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# 0x00007F916DC033C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 26# 0x00007FB3B89CD3C6 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 @@ -34516,50 +34386,49 @@ 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# 0x00007F916E3E0CA8 in /lib/x86_64-linux-gnu/libc.so.6 +195: 58# 0x00007FB3B91AACA8 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: -219/236 Test #95: testEnumeration ........................ Passed 13.51 sec -195: ......[00:25:10] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -195: [00:25:10] ERROR: Smiles parse error on line 0 -195: [00:25:10] ERROR: Cannot create molecule from : 'c1ccccc' -195: [00:25:10] SMILES Parse Error: extra open parentheses while parsing: C(C -195: [00:25:10] SMILES Parse Error: check for mistakes around position 2: -195: [00:25:10] C(C -195: [00:25:10] ~^ -195: [00:25:10] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' -195: [00:25:10] ERROR: Smiles parse error on line 3 -195: [00:25:10] ERROR: Cannot create molecule from : 'C(C' -195: [00:25:10] Explicit valence for atom # 1 C, 5, is greater than permitted -195: [00:25:10] ERROR: Could not sanitize molecule on line 6 -195: [00:25:10] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted -195: [00:25:10] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -195: [00:25:10] ERROR: Smiles parse error on line 0 -195: [00:25:10] ERROR: Cannot create molecule from : 'c1ccccc' -195: [00:25:10] SMILES Parse Error: extra open parentheses while parsing: C(C -195: [00:25:10] SMILES Parse Error: check for mistakes around position 2: -195: [00:25:10] C(C -195: [00:25:10] ~^ -195: [00:25:10] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' -195: [00:25:10] ERROR: Smiles parse error on line 3 -195: [00:25:10] ERROR: Cannot create molecule from : 'C(C' -195: [00:25:10] SMILES Parse Error: unclosed ring for input: 'C1C(Cl)CCCC' -195: [00:25:10] ERROR: Smiles parse error on line 6 -195: [00:25:10] ERROR: Cannot create molecule from : 'C1C(Cl)CCCC' -195: [00:25:10] Explicit valence for atom # 1 F, 2, is greater than permitted -195: [00:25:10] ERROR: Could not sanitize molecule ending on line 21 -195: [00:25:10] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -195: [00:25:10] ERROR: EOF hit while reading atoms -195: [00:25:10] ERROR: moving to the beginning of the next molecule -195: [00:25:10] Explicit valence for atom # 1 F, 2, is greater than permitted -195: [00:25:10] ERROR: Could not sanitize molecule ending on line 21 -195: [00:25:10] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -195: [00:25:10] ERROR: EOF hit while reading atoms -195: [00:25:10] ERROR: moving to the beginning of the next molecule -195: ....[00:25:10] +195: ......[20:24:27] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +195: [20:24:27] ERROR: Smiles parse error on line 0 +195: [20:24:27] ERROR: Cannot create molecule from : 'c1ccccc' +195: [20:24:27] SMILES Parse Error: extra open parentheses while parsing: C(C +195: [20:24:27] SMILES Parse Error: check for mistakes around position 2: +195: [20:24:27] C(C +195: [20:24:27] ~^ +195: [20:24:27] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' +195: [20:24:27] ERROR: Smiles parse error on line 3 +195: [20:24:27] ERROR: Cannot create molecule from : 'C(C' +195: [20:24:27] Explicit valence for atom # 1 C, 5, is greater than permitted +195: [20:24:27] ERROR: Could not sanitize molecule on line 6 +195: [20:24:27] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted +195: [20:24:27] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +195: [20:24:27] ERROR: Smiles parse error on line 0 +195: [20:24:27] ERROR: Cannot create molecule from : 'c1ccccc' +195: [20:24:27] SMILES Parse Error: extra open parentheses while parsing: C(C +195: [20:24:27] SMILES Parse Error: check for mistakes around position 2: +195: [20:24:27] C(C +195: [20:24:27] ~^ +195: [20:24:27] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' +195: [20:24:27] ERROR: Smiles parse error on line 3 +195: [20:24:27] ERROR: Cannot create molecule from : 'C(C' +195: [20:24:27] SMILES Parse Error: unclosed ring for input: 'C1C(Cl)CCCC' +195: [20:24:27] ERROR: Smiles parse error on line 6 +195: [20:24:27] ERROR: Cannot create molecule from : 'C1C(Cl)CCCC' +195: [20:24:27] Explicit valence for atom # 1 F, 2, is greater than permitted +195: [20:24:27] ERROR: Could not sanitize molecule ending on line 21 +195: [20:24:27] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +195: [20:24:27] ERROR: EOF hit while reading atoms +195: [20:24:27] ERROR: moving to the beginning of the next molecule +195: [20:24:27] Explicit valence for atom # 1 F, 2, is greater than permitted +195: [20:24:27] ERROR: Could not sanitize molecule ending on line 21 +195: [20:24:27] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +195: [20:24:27] ERROR: EOF hit while reading atoms +195: [20:24:27] ERROR: moving to the beginning of the next molecule +195: ....[20:24:27] 195: 195: **** 195: Pre-condition Violation @@ -34573,7 +34442,7 @@ 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# 0x00007F916DC0662C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 5# 0x00007FB3B89D062C 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 +34453,17 @@ 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# 0x00007F916B3B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 17# 0x00007F916B3B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 18# 0x00007F916B3B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 19# 0x00007F916B3B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 20# 0x00007F916B3B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 16# 0x00007FB3B61B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 17# 0x00007FB3B61B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 18# 0x00007FB3B61B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 19# 0x00007FB3B61B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 20# 0x00007FB3B61B7933 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# 0x00007F916DC033C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 26# 0x00007FB3B89CD3C6 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 +34495,13 @@ 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# 0x00007F916E3E0CA8 in /lib/x86_64-linux-gnu/libc.so.6 +195: 58# 0x00007FB3B91AACA8 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: .............[00:25:10] +195: .............[20:24:27] 195: 195: **** 195: Range Error @@ -34646,7 +34515,7 @@ 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# 0x00007F916DC0662C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 5# 0x00007FB3B89D062C 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 +34526,17 @@ 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# 0x00007F916B3B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 17# 0x00007F916B3B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 18# 0x00007F916B3B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 19# 0x00007F916B3B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 20# 0x00007F916B3B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 16# 0x00007FB3B61B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 17# 0x00007FB3B61B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 18# 0x00007FB3B61B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 19# 0x00007FB3B61B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 20# 0x00007FB3B61B7933 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# 0x00007F916DC033C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 26# 0x00007FB3B89CD3C6 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 @@ -34699,120 +34568,329 @@ 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# 0x00007F916E3E0CA8 in /lib/x86_64-linux-gnu/libc.so.6 +195: 58# 0x00007FB3B91AACA8 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: ...[00:25:10] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -195: ............................[00:25:10] SMILES Parse Error: unclosed ring for input: 'C1CC' +195: ...[20:24:27] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +195: ............................[20:24:27] 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: 643 -195: ..[00:25:10] WARNING: not removing hydrogen atom without neighbors -195: [00:25:10] WARNING: not removing hydrogen atom with dummy atom neighbors -195: [00:25:10] WARNING: not removing hydrogen atom with wedged bond -195: [00:25:10] WARNING: not removing hydrogen atom without neighbors -195: [00:25:10] WARNING: not removing hydrogen atom with dummy atom neighbors -195: ......[00:25:10] Explicit valence for atom # 1 F, 2, is greater than permitted -195: [00:25:10] Can't kekulize mol. Unkekulized atoms: 0 1 2 -195: .[00:25:10] Explicit valence for atom # 1 F, 2, is greater than permitted -195: [00:25:10] Explicit valence for atom # 1 F, 2, is greater than permitted -195: [00:25:10] Explicit valence for atom # 1 F, 2, is greater than permitted -195: [00:25:10] Explicit valence for atom # 1 F, 2, is greater than permitted -195: [00:25:10] Can't kekulize mol. Unkekulized atoms: 0 1 2 -195: [00:25:10] Can't kekulize mol. Unkekulized atoms: 0 1 2 -195: [00:25:10] Can't kekulize mol. Unkekulized atoms: 0 1 2 -195: ..........[00:25:10] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname -195: [00:25:10] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' -195: .[00:25:10] SMILES Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname -195: [00:25:10] SMILES Parse Error: check for mistakes around position 4: -195: [00:25:10] CCC |$foo;;bar$| ourname -195: [00:25:10] ~~~^ -195: [00:25:10] SMILES Parse Error: Failed parsing SMILES 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' -195: ..[00:25:10] SMILES Parse Error: syntax error while parsing: error -195: [00:25:10] SMILES Parse Error: check for mistakes around position 1: -195: [00:25:10] error -195: [00:25:10] ^ -195: [00:25:10] SMILES Parse Error: Failed parsing SMILES 'error' for input: 'error' -195: [00:25:10] SMILES Parse Error: Failed parsing SMILES 'd' for input: 'd' -195: [00:25:10] SMARTS Parse Error: Failed parsing SMARTS 'error' for input: 'error' -195: [00:25:10] SMARTS Parse Error: Failed parsing SMARTS 'd' for input: 'd' -195: .........................[00:25:10] SMILES Parse Error: syntax error while parsing: garbage_0 -195: [00:25:10] SMILES Parse Error: check for mistakes around position 1: -195: [00:25:10] garbage_0 -195: [00:25:10] ^ -195: [00:25:10] SMILES Parse Error: Failed parsing SMILES 'garbage_0' for input: 'garbage_0' -195: [00:25:10] SMILES Parse Error: syntax error while parsing: garbage_2 -195: [00:25:10] SMILES Parse Error: check for mistakes around position 1: -195: [00:25:10] garbage_2 -195: [00:25:10] ^ -195: [00:25:10] SMILES Parse Error: Failed parsing SMILES 'garbage_2' for input: 'garbage_2' -195: [00:25:10] SMILES Parse Error: syntax error while parsing: garbage_4 -195: [00:25:10] SMILES Parse Error: check for mistakes around position 1: -195: [00:25:10] garbage_4 -195: [00:25:10] ^ -195: [00:25:10] SMILES Parse Error: Failed parsing SMILES 'garbage_4' for input: 'garbage_4' +195: ..[20:24:27] WARNING: not removing hydrogen atom without neighbors +195: [20:24:27] WARNING: not removing hydrogen atom with dummy atom neighbors +195: [20:24:27] WARNING: not removing hydrogen atom with wedged bond +195: [20:24:27] WARNING: not removing hydrogen atom without neighbors +195: [20:24:27] WARNING: not removing hydrogen atom with dummy atom neighbors +195: ......[20:24:28] Explicit valence for atom # 1 F, 2, is greater than permitted +195: [20:24:28] Can't kekulize mol. Unkekulized atoms: 0 1 2 +195: .[20:24:28] Explicit valence for atom # 1 F, 2, is greater than permitted +195: [20:24:28] Explicit valence for atom # 1 F, 2, is greater than permitted +195: [20:24:28] Explicit valence for atom # 1 F, 2, is greater than permitted +195: [20:24:28] Explicit valence for atom # 1 F, 2, is greater than permitted +195: [20:24:28] Can't kekulize mol. Unkekulized atoms: 0 1 2 +195: [20:24:28] Can't kekulize mol. Unkekulized atoms: 0 1 2 +195: [20:24:28] Can't kekulize mol. Unkekulized atoms: 0 1 2 +195: ..........[20:24:28] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname +195: [20:24:28] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' +195: .[20:24:28] SMILES Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname +195: [20:24:28] SMILES Parse Error: check for mistakes around position 4: +195: [20:24:28] CCC |$foo;;bar$| ourname +195: [20:24:28] ~~~^ +195: [20:24:28] SMILES Parse Error: Failed parsing SMILES 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' +195: ..[20:24:28] SMILES Parse Error: syntax error while parsing: error +195: [20:24:28] SMILES Parse Error: check for mistakes around position 1: +195: [20:24:28] error +195: [20:24:28] ^ +195: [20:24:28] SMILES Parse Error: Failed parsing SMILES 'error' for input: 'error' +195: [20:24:28] SMILES Parse Error: Failed parsing SMILES 'd' for input: 'd' +195: [20:24:28] SMARTS Parse Error: Failed parsing SMARTS 'error' for input: 'error' +195: [20:24:28] SMARTS Parse Error: Failed parsing SMARTS 'd' for input: 'd' +195: .........................[20:24:28] SMILES Parse Error: syntax error while parsing: garbage_0 +195: [20:24:28] SMILES Parse Error: check for mistakes around position 1: +195: [20:24:28] garbage_0 +195: [20:24:28] ^ +195: [20:24:28] SMILES Parse Error: Failed parsing SMILES 'garbage_0' for input: 'garbage_0' +195: [20:24:28] SMILES Parse Error: syntax error while parsing: garbage_2 +195: [20:24:28] SMILES Parse Error: check for mistakes around position 1: +195: [20:24:28] garbage_2 +195: [20:24:28] ^ +195: [20:24:28] SMILES Parse Error: Failed parsing SMILES 'garbage_2' for input: 'garbage_2' +195: [20:24:28] SMILES Parse Error: syntax error while parsing: garbage_4 +195: [20:24:28] SMILES Parse Error: check for mistakes around position 1: +195: [20:24:28] garbage_4 +195: [20:24:28] ^ +195: [20:24:28] SMILES Parse Error: Failed parsing SMILES 'garbage_4' for input: 'garbage_4' 195: ............ 195: ---------------------------------------------------------------------- -195: Ran 279 tests in 10.233s +195: Ran 279 tests in 10.413s 195: 195: OK 195: supplier: 195: supplier: 195: supplier: -220/236 Test #195: pyGraphMolWrap ......................... Passed 11.08 sec -152: ...[00:25:10] Molecule does not have explicit Hs. Consider calling AddHs() -152: [00:25:10] Molecule does not have explicit Hs. Consider calling AddHs() -152: [00:25:10] Molecule does not have explicit Hs. Consider calling AddHs() -152: [00:25:10] Molecule does not have explicit Hs. Consider calling AddHs() -152: [00:25:10] Molecule does not have explicit Hs. Consider calling AddHs() +219/236 Test #195: pyGraphMolWrap ......................... Passed 11.71 sec +183: [20:24:28] ------------------------------------- +183: [20:24:28] Results do not depend on numThreads (all same) +183: [20:24:28] ------------------------------------- +183: [20:24:28] testTautomerQueries +183: [20:24:28] Pattern fingerprints for tautomersearch aren't tautomer fingerprints, ignoring... +183: [20:24:28] ------------------------------------- +183: [20:24:28] github3881 recursive smarts with rings +220/236 Test #183: substructLibraryTest ................... Passed 13.04 sec +185: ......[20:24:28] +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# 0x00007FE08AA5D1D5 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# 0x00007FE08CF0462C 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# 0x00007FE08A9B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +185: 21# 0x00007FE08A9B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +185: 22# 0x00007FE08A9B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +185: 23# 0x00007FE08A9B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +185: 24# 0x00007FE08A9B7933 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# 0x00007FE08CF013C6 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# 0x00007FE08D847CA8 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: [20:24:28] +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# 0x00007FE08A4E6800 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# 0x00007FE08AA5D1D5 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# 0x00007FE08CF0462C 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# 0x00007FE08A9B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +185: 22# 0x00007FE08A9B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +185: 23# 0x00007FE08A9B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +185: 24# 0x00007FE08A9B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +185: 25# 0x00007FE08A9B7933 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# 0x00007FE08CF013C6 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# 0x00007FE08D847CA8 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: ...[20:24:28] Molecule does not have explicit Hs. Consider calling AddHs() +152: [20:24:28] Molecule does not have explicit Hs. Consider calling AddHs() +152: [20:24:28] Molecule does not have explicit Hs. Consider calling AddHs() +152: [20:24:28] Molecule does not have explicit Hs. Consider calling AddHs() +152: [20:24:28] Molecule does not have explicit Hs. Consider calling AddHs() 152: ... 152: ---------------------------------------------------------------------- -152: Ran 19 tests in 12.799s +152: Ran 19 tests in 14.500s 152: 152: OK 152: Testing MolAlign Wrappers -221/236 Test #152: pyMolAlign ............................. Passed 13.19 sec -185: ............. -185: ---------------------------------------------------------------------- -185: Ran 19 tests in 12.183s -185: -185: OK -185: Testing atom rings -185: testing bond rings -185: searching atom rings -185: searching bond rings -185: done -222/236 Test #185: pySubstructLibrary ..................... Passed 12.58 sec -173: [00:25:12] Complex queries can be slow. -173: [00:25:12] Complex queries can be slow. -173: [00:25:12] Complex queries can be slow. -173: [00:25:12] Complex queries can be slow. -173: [00:25:12] Complex queries can be slow. -173: [00:25:12] Complex queries can be slow. -173: [00:25:12] Complex queries can be slow. -173: [00:25:12] Complex queries can be slow. -51: Randomness seeded to: 1324227649 +221/236 Test #152: pyMolAlign ............................. Passed 14.87 sec +173: [20:24:29] Complex queries can be slow. +173: [20:24:29] Complex queries can be slow. +173: [20:24:29] Complex queries can be slow. +173: [20:24:29] Complex queries can be slow. +173: [20:24:29] Complex queries can be slow. +173: [20:24:29] Complex queries can be slow. +29: Checking against /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +173: [20:24:30] Complex queries can be slow. +29: All 191 tests passed +51: Randomness seeded to: 1550557947 51: =============================================================================== 51: All tests passed (14835 assertions in 14 test cases) 51: -223/236 Test #51: canonTestsCatch ........................ Passed 16.42 sec -173: [00:25:12] Complex queries can be slow. -173: [00:25:13] Complex queries can be slow. +222/236 Test #51: canonTestsCatch ........................ Passed 17.41 sec +29: +29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.smi... +173: [20:24:30] Complex queries can be slow. +173: [20:24:30] Complex queries can be slow. +173: [20:24:30] Complex queries can be slow. +173: [20:24:30] Complex queries can be slow. +173: [20:24:30] Complex queries can be slow. 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 15.20 seconds -224/236 Test #163: testFMCS ............................... Passed 15.26 sec -173: [00:25:13] Complex queries can be slow. -173: [00:25:13] Complex queries can be slow. -173: [00:25:13] Complex queries can be slow. +163: TOTAL Time elapsed 16.57 seconds +223/236 Test #163: testFMCS ............................... Passed 16.63 sec +173: [20:24:30] Complex queries can be slow. +173: [20:24:30] Complex queries can be slow. +173: [20:24:30] Complex queries can be slow. +185: ............. +185: ---------------------------------------------------------------------- +185: Ran 19 tests in 15.089s +185: +185: OK +185: Testing atom rings +185: testing bond rings +185: searching atom rings +185: searching bond rings +185: done +224/236 Test #185: pySubstructLibrary ..................... Passed 15.44 sec +173: [20:24:31] Complex queries can be slow. +173: [20:24:31] Complex queries can be slow. +173: [20:24:31] Complex queries can be slow. +173: [20:24:31] Complex queries can be slow. +173: =============================================================================== +173: All tests passed (121 assertions in 17 test cases) +173: +225/236 Test #173: testSynthonSpaceSubstructureSearch ..... Passed 16.88 sec +150: --------------------------------- +150: test O3A multithreading bug +150: +150: --------------------------------- +150: testCrippenO3A multithreading +150: +150: generating reference data +150: processing +150: launch :0 +150: launch :1 +150: launch :2 +150: launch :3 29: Checking against /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -173: [00:25:13] Complex queries can be slow. +148: .........[20:24:33] Molecule does not have explicit Hs. Consider calling AddHs() +148: .[20:24:33] Molecule does not have explicit Hs. Consider calling AddHs() +148: [20:24:33] Molecule does not have explicit Hs. Consider calling AddHs() +148: [20:24:33] Molecule does not have explicit Hs. Consider calling AddHs() +148: [20:24:33] Molecule does not have explicit Hs. Consider calling AddHs() +148: [20:24:33] Molecule does not have explicit Hs. Consider calling AddHs() +148: [20:24:33] Molecule does not have explicit Hs. Consider calling AddHs() +148: [20:24:33] Molecule does not have explicit Hs. Consider calling AddHs() +148: [20:24:33] Molecule does not have explicit Hs. Consider calling AddHs() +148: [20:24:33] Molecule does not have explicit Hs. Consider calling AddHs() +148: [20:24:33] Molecule does not have explicit Hs. Consider calling AddHs() +148: .[20:24:33] Molecule does not have explicit Hs. Consider calling AddHs() +148: [20:24:33] Molecule does not have explicit Hs. Consider calling AddHs() +148: [20:24:33] Molecule does not have explicit Hs. Consider calling AddHs() +148: [20:24:33] Molecule does not have explicit Hs. Consider calling AddHs() +148: [20:24:33] Molecule does not have explicit Hs. Consider calling AddHs() +148: [20:24:33] Molecule does not have explicit Hs. Consider calling AddHs() +148: [20:24:33] Molecule does not have explicit Hs. Consider calling AddHs() +148: [20:24:33] Molecule does not have explicit Hs. Consider calling AddHs() +148: [20:24:33] Molecule does not have explicit Hs. Consider calling AddHs() +148: [20:24:33] Molecule does not have explicit Hs. Consider calling AddHs() 29: All 191 tests passed 29: done 29: ------------------------------------- @@ -34827,70 +34905,31 @@ 29: done 29: ------------------------------------- 29: Unit test for MMFF butane scan. -173: [00:25:13] Complex queries can be slow. 29: done -225/236 Test #29: testMMFFForceField ..................... Passed 17.55 sec -173: [00:25:13] Complex queries can be slow. -173: [00:25:13] Complex queries can be slow. -150: --------------------------------- -150: test O3A multithreading bug -150: -150: --------------------------------- -150: testCrippenO3A multithreading -150: -150: generating reference data -173: [00:25:14] Complex queries can be slow. -173: [00:25:14] Complex queries can be slow. -173: =============================================================================== -173: All tests passed (121 assertions in 17 test cases) -173: -226/236 Test #173: testSynthonSpaceSubstructureSearch ..... Passed 16.18 sec -150: processing -150: launch :0 -150: launch :1 -150: launch :2 -150: launch :3 -210: [00:25:15] Explicit valence for atom # 0 Br, 1, is greater than permitted +226/236 Test #29: testMMFFForceField ..................... Passed 21.15 sec +210: [20:24:34] 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 14.56 sec -148: .........[00:25:15] Molecule does not have explicit Hs. Consider calling AddHs() -148: .[00:25:15] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:25:15] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:25:15] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:25:15] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:25:15] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:25:15] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:25:15] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:25:15] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:25:15] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:25:15] Molecule does not have explicit Hs. Consider calling AddHs() -148: .[00:25:15] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:25:15] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:25:15] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:25:15] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:25:15] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:25:15] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:25:15] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:25:15] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:25:15] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:25:15] Molecule does not have explicit Hs. Consider calling AddHs() +227/236 Test #210: molStandardizeCatchTest ................ Passed 16.41 sec 148: ... 148: ---------------------------------------------------------------------- -148: Ran 22 tests in 20.054s +148: Ran 22 tests in 23.262s 148: 148: OK -228/236 Test #148: pyDistGeomHelpers ...................... Passed 20.52 sec +228/236 Test #148: pyDistGeomHelpers ...................... Passed 23.65 sec 150: --------------------------------- 150: test getO3AForProbeConfs 150: 150: *********************************************************** -229/236 Test #150: testO3AAlign ........................... Passed 24.24 sec -5: [00:25:22] Finished: testMultipleTimes() -5: [00:25:22] +229/236 Test #150: testO3AAlign ........................... Passed 25.83 sec +5: [20:24:40] Finished: testMultipleTimes() +5: [20:24:40] 5: ----------------------------------------- -230/236 Test #5: testConcurrentQueue .................... Passed 26.46 sec +230/236 Test #5: testConcurrentQueue .................... Passed 28.26 sec +147: [20:24:44] UFFTYPER: Unrecognized atom type: S_6+6 (0) +147: [20:24:44] UFFTYPER: Warning: hybridization set to SP3 for atom 0 +147: [20:24:44] UFFTYPER: Unrecognized charge state for atom: 0 236: DbCLI/UnitTestDbCLI.py ............ [100%] 236: 236: =============================== warnings summary =============================== @@ -34899,30 +34938,23 @@ 236: decBase = declarative_base() 236: 236: -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html -236: ======================== 12 passed, 1 warning in 21.97s ======================== -231/236 Test #236: pythonProjectTests ..................... Passed 22.71 sec -147: [00:25:26] UFFTYPER: Unrecognized atom type: S_6+6 (0) -147: [00:25:26] UFFTYPER: Warning: hybridization set to SP3 for atom 0 -147: [00:25:26] UFFTYPER: Unrecognized charge state for atom: 0 -146: [00:25:35] done -146: [00:25:35] --------------------------------- -146: [00:25:35] test github issue 256: handling of zero-atom molecules +236: ======================== 12 passed, 1 warning in 32.19s ======================== +231/236 Test #236: pythonProjectTests ..................... Passed 32.82 sec +146: [20:24:52] done +146: [20:24:52] --------------------------------- +146: [20:24:52] test github issue 256: handling of zero-atom molecules 146: -146: [00:25:35] --------------------------------- -146: [00:25:35] test embedder callback function -146: [00:25:35] --------------------------------- -146: [00:25:35] test multi-threaded multi-conf embedding +146: [20:24:52] --------------------------------- +146: [20:24:52] test embedder callback function +146: [20:24:52] --------------------------------- +146: [20:24:52] test multi-threaded multi-conf embedding 146: -146: [00:25:38] --------------------------------- -146: [00:25:38] test github issue 563: Incorrect ring stereochemistry after embedding +146: [20:24:54] --------------------------------- +146: [20:24:54] test github issue 563: Incorrect ring stereochemistry after embedding 146: 146: CNC[C@H]1CC[C@H](C[NH3+])CC1 -171: =============================================================================== -171: All tests passed (93 assertions in 5 test cases) -171: -232/236 Test #171: testRascalCluster ...................... Passed 40.90 sec -146: [00:25:39] --------------------------------- -146: [00:25:39] test github issue 568: Incorrect stereochemistry after embedding +146: [20:24:56] --------------------------------- +146: [20:24:56] 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 @@ -34934,6 +34966,10 @@ 146: CCS[C@@H]1[C@@H](N)[C@@H](O)[C@@H](O)[C@H]1O 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 +171: =============================================================================== +171: All tests passed (93 assertions in 5 test cases) +171: +232/236 Test #171: testRascalCluster ...................... Passed 47.20 sec 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 @@ -34944,13 +34980,12 @@ 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 -146: COc1cc2c(cc1OC)[C@@H]1C[C@@H]3C[C@H](O)CC[C@@H]3CN1CC2 170: =============================================================================== 170: All tests passed (3590 assertions in 35 test cases) 170: -233/236 Test #170: testRascalMCES ......................... Passed 51.21 sec -146: N#C[C@@H]1C[C@@H]2CN3CCc4cc5c(cc4[C@@H]3C[C@@H]2C[C@@H]1O)OCO5 -147: [00:25:50] Interrupted, cancelling conformer generation +233/236 Test #170: testRascalMCES ......................... Passed 52.45 sec +146: COc1cc2c(cc1OC)[C@@H]1C[C@@H]3C[C@H](O)CC[C@@H]3CN1CC2 +147: [20:25:08] 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] @@ -34983,58 +35018,59 @@ 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: COC(=O)[C@@H]1C[C@](C)(C(=O)O)NC(=O)N1 147: =============================================================================== 147: All tests passed (12742 assertions in 21 test cases) 147: -234/236 Test #147: distGeomHelpersCatch ................... Passed 53.09 sec +234/236 Test #147: distGeomHelpersCatch ................... Passed 54.71 sec +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 146: CC(=O)OC1=C(Sc2ccccc2)C[C@H]2Cc3cc4cccc(O)c4c(O)c3C(=O)[C@H]2C1 146: Nc1ncnc2c1ncn2[C@@H]1C[C@H](CO)[C@@H](O)C1 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: [00:25:58] Molecule does not have explicit Hs. Consider calling AddHs() -146: [00:25:53] --------------------------------- -146: [00:25:53] test github issue 696: Bad 1-4 bounds matrix elements in highly constrained system -146: [00:25:53] --------------------------------- -146: [00:25:53] More ChEMBL molecules failing bounds smoothing. -146: [00:25:53] --------------------------------- -146: [00:25:53] ugly conformations can be generated for highly constrained ring systems. -146: [00:25:53] --------------------------------- -146: [00:25:53] test embed parameters structure. -146: [00:25:53] --------------------------------- -146: [00:25:53] test github 1227: Hs being used in RMSD filtering. -146: [00:25:53] --------------------------------- -146: [00:25:53] Failure to embed larger aromatic rings. -146: [00:25:55] --------------------------------- -146: [00:25:55] Deterministic with large random seeds -146: [00:25:57] --------------------------------- -146: [00:25:57] Github #1990: seg fault after RemoveHs -146: [00:25:57] --------------------------------- -146: [00:25:57] Github #2246: Use coordMap when starting embedding from random coords -146: [00:25:58] --------------------------------- -146: [00:25:58] Providing a distance bounds matrix. -146: [00:25:58] --------------------------------- -146: [00:25:58] Disabling fragmentation. -146: [00:25:58] --------------------------------- -146: [00:25:58] Using symmetry in conformation pruning. -146: [00:25:58] --------------------------------- -146: [00:25:58] Force trans amides. -146: [00:25:58] --------------------------------- -146: [00:25:58] test missing Hs warning. -146: [00:25:58] --------------------------------- -146: [00:25:58] basic H bond support. -146: [00:25:58] ******************************************************* -235/236 Test #146: testDistGeomHelpers .................... Passed 61.17 sec -174: Randomness seeded to: 3374938584 +146: [20:25:17] Molecule does not have explicit Hs. Consider calling AddHs() +146: [20:25:12] --------------------------------- +146: [20:25:12] test github issue 696: Bad 1-4 bounds matrix elements in highly constrained system +146: [20:25:12] --------------------------------- +146: [20:25:12] More ChEMBL molecules failing bounds smoothing. +146: [20:25:12] --------------------------------- +146: [20:25:12] ugly conformations can be generated for highly constrained ring systems. +146: [20:25:12] --------------------------------- +146: [20:25:12] test embed parameters structure. +146: [20:25:12] --------------------------------- +146: [20:25:12] test github 1227: Hs being used in RMSD filtering. +146: [20:25:12] --------------------------------- +146: [20:25:12] Failure to embed larger aromatic rings. +146: [20:25:14] --------------------------------- +146: [20:25:14] Deterministic with large random seeds +146: [20:25:16] --------------------------------- +146: [20:25:16] Github #1990: seg fault after RemoveHs +146: [20:25:16] --------------------------------- +146: [20:25:16] Github #2246: Use coordMap when starting embedding from random coords +146: [20:25:17] --------------------------------- +146: [20:25:17] Providing a distance bounds matrix. +146: [20:25:17] --------------------------------- +146: [20:25:17] Disabling fragmentation. +146: [20:25:17] --------------------------------- +146: [20:25:17] Using symmetry in conformation pruning. +146: [20:25:17] --------------------------------- +146: [20:25:17] Force trans amides. +146: [20:25:17] --------------------------------- +146: [20:25:17] test missing Hs warning. +146: [20:25:17] --------------------------------- +146: [20:25:17] basic H bond support. +146: [20:25:17] ******************************************************* +235/236 Test #146: testDistGeomHelpers .................... Passed 64.04 sec +174: Randomness seeded to: 1411954214 174: =============================================================================== 174: All tests passed (28 assertions in 2 test cases) 174: -236/236 Test #174: testSynthonSpaceRascalSearch ........... Passed 63.32 sec +236/236 Test #174: testSynthonSpaceRascalSearch ........... Passed 66.26 sec 100% tests passed, 0 tests failed out of 236 -Total Test time (real) = 65.40 sec +Total Test time (real) = 68.46 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 +35080,7 @@ 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 +35091,1278 @@ /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: /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/retest.txt +-- 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/cactvs.py +-- 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/__init__.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils/spiral.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/TestRunner.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/Chem --- 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/Pharm2D --- 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/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/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/FeatFinderCLI.py --- Installing: 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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: /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/examples/tkCanvas-with-scrollbars.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/sping/TK -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/TK/__init__.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/TK/pidTK.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/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: /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/EnumerateStereoisomers.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/SimpleEnum +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/SimpleEnum/Enumerator.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/SimpleEnum/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/EnumerateHeterocycles.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/FilterCatalog.py +-- Installing: /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: /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/Pharmacophore.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/EmbedLib.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/TorsionFingerprints.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/BuildFragmentCatalog.py +-- Installing: /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/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: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Fingerprints/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Fingerprints/ClusterMols.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Fingerprints/MolSimilarity.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Fingerprints/FingerprintMols.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Fingerprints/DbFpSupplier.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/PropertyMol.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/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: 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/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: 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/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: 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/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: /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_56.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_23.png -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_29.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_58.png -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_51.png --- 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: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_16.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_53.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_17.png -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_43.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_12.png +-- 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: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_13.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_14.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_22.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_28.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_18.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_56.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_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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+-- 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: /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-MutipleCores.ipynb --- 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.png --- 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.inkscape.svg --- 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.lrg.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/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/Book_jp/index.rst +-- 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/introduction_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/The_RDKit_Book_jp.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/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: /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/gsocGeneralFileReader.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/SGroups.md -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Code/images --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_and2_base.png --- Installing: /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/images/enhanced_stereo_and1_cis_expand.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_or1_trans_base.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_abs_and_expand.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_and2_expand.png -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_cis_base.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_or1_or2_base.png -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_or1_cis_base.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_or1_or2_base.png +-- 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/mfp2_bit872.svg +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/substruct_search_parameters1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_highlights_1.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/atrop_example5.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/picture_10.jpg +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_0_im2.png +-- Installing: 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/build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/similarity_map_charges.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/RDKitCB_2_im0.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/RDKitCB_6_im1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/cdk2_mol2.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/RDKitCB_0_im1.png +-- Installing: 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/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: /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/data/sample.smi +-- 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_subs_output.txt +-- 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/MolVS +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/MolVS/molvs_cli.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/efgs -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/efgs/efgs.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/efgs/README.md --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/efgs/ch33query.sql -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/efgs/try_efgs.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/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/efgs/ch33query.sql +-- 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/setup.py +-- 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/pytest.ini +-- 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/data +-- 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/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/freewilson.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/M_Kossner -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/M_Kossner/Frames.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/M_Kossner/BaseFeatures_DIP2_NoMicrospecies.fdef -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/M_Kossner/README --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters --- Installing: 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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 +36408,12 @@ -- 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 +37034,10 @@ 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 +37082,11 @@ 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 +37713,22 @@ 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 errstart: it's probably a plugin +dpkg-shlibdeps: warning: debian/postgresql-17-rdkit/usr/lib/postgresql/17/lib/rdkit.so contains an unresolvable reference to symbol pg_snprintf: 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 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_RuntimeError 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 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_SetObject 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 PyExc_ValueError used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries -dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries -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 PyLong_FromLong 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 PyErr_SetString 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: 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 +37736,22 @@ 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 librdkit-dev: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package rdkit-doc: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package rdkit-data: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: 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 dh_md5sums -O--buildsystem=cmake dh_builddeb -O--buildsystem=cmake -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 'librdkit1t64-dbgsym' in '../librdkit1t64-dbgsym_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 'postgresql-17-rdkit-dbgsym' in '../postgresql-17-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 'python3-rdkit' in '../python3-rdkit_202503.1-4_amd64.deb'. +dpkg-deb: building package 'rdkit-doc' in '../rdkit-doc_202503.1-4_all.deb'. +dpkg-deb: building package 'rdkit-data' in '../rdkit-data_202503.1-4_all.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 +37759,14 @@ 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/1069129/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1069129/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/2042499 and its subdirectories -I: Current time: Thu Aug 20 00:29:38 -12 2026 -I: pbuilder-time-stamp: 1787228978 +I: removing directory /srv/workspace/pbuilder/1069129 and its subdirectories +I: Current time: Fri Jul 18 20:30:05 +14 2025 +I: pbuilder-time-stamp: 1752820205